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metacat / README @ 8440

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#
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#  '$RCSfile$'
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#   '$Author: leinfelder $'
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# '$Revision: 8440 $'
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#     '$Date: 2013-12-19 08:53:22 -0800 (Thu, 19 Dec 2013) $'
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#
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Metacat: XML Metadata and Data Management System
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------------------------------------------------                      
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Version: 2.3.1 Release
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Send feedback and bugs to: metacat-dev@ecoinformatics.org
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                           http://bugzilla.ecoinformatics.org
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Contributors: Matt Jones (jones@nceas.ucsb.edu)
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              Chad Berkley (berkley@nceas.ucsb.edu)
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              Jing Tao (tao@nceas.ucsb.edu)
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              Jivka Bojilova (bojilova@nceas.ucsb.edu)
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              Dan Higgins (higgins@nceas.ucsb.edu)
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              Saurabh Garg (sgarg@nceas.ucsb.edu)
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              Duane Costa (dcosta@lternet.edu)
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              Veronique Connolly (connolly@nceas.ucsb.edu)
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              Chris Jones (cjones@msi.ucsb.edu)
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              John Harris (harris@nceas.ucsb.edu)
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              Callie Bowdish (bowdish@ecoinformatics.org)
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              Will Tyburczy (tyburczy@ecoinformatics.org)
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              Matthew Perry (perry@nceas.ucsb.edu)
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              Chad Burt (underbluewaters@gmail.com)
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              Ben Leinfelder (leinfelder@nceas.ucsb.edu)
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              Chris Barteau (barteau@nceas.ucsb.edu)
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              Shaun Walbridge (walbridge@nceas.ucsb.edu)
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              Michael Daigle (daigle@nceas.ucsb.edu) 
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              Lauren Walker (walker@nceas.ucsb.edu) 
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Patch contributors:
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              Andrea Chadden (chadden@nceas.ucsb.edu)
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              Johnoel Ancheta (johnoel@hawaii.edu)
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              Owen Jones (owen.jones@imperial.ac.uk)
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Metacat is a flexible database storage system for XML formatted
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documents and associated binary files. Metacat models the structure of the
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XML document, therefore allowing storage of XML documents with arbitrary
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schemas. Metacat supports several databases on the back-end, including Oracle,
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PostgreSQL and SQL Server (limited).  The server supports XML document
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storage, retrieval, query, validation, and transformation (using the XSLT
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stylesheet language).  In addition, there is a mechanism for replicating the
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database to other metacat instances for backup and load balancing purposes.
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Metacat currently uses an LDAP database for authenticating users, but was
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written to accomodate other authentication services as well.
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Installation
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------------
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See the file "docs/install.html" for detailed instructions
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for your OS.
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Release Notes for 2.3.1:
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------------------------
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This is a minor patch release to fix an issue that arises when
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Metacat is operating as a DataONE Coordinating Node.
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See: https://projects.ecoinformatics.org/ecoinfo/issues/6315
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Release Notes for 2.3.0:
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------------------------
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This release adds solr indexing features to metacat-index 
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for querying and sorting by authors and taxonomic coverage.
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Also includes:
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* Control over the log level from the SOLR libraries using Metacat's
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log4j file.
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* access_log DB indexes for better log reporting performance 
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via the DataONE API
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* Provide 'reindexall' action instead of 'reindex' without a 'pid' parameter.
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Release Notes for 2.2.1:
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------------------------
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This is a critical patch release of Metacat that includes addresses
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a bug in file stream handling. It is recommended for all Metacat deployments.
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Release Notes for 2.2.0:
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------------------------
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This is a major release of Metacat that includes a new customizable UI and 
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improved LDAP account management features
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Release Notes for 2.1.1:
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------------------------
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This is a minor patch release of Metacat that addresses
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a bug in DOI publishing.
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Release Notes for 2.1.0:
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------------------------
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This is a major release of Metacat that includes a SOLR-based search feature
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* Optional SOLR search index
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* Client certificate delegation (using a service provider like CILogon)
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Release Notes for 2.0.8:
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------------------------
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This is a patch release for Metacat
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* Enforce DataONE prohibition on whitespace in identifiers
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* Use unique filenames for Registry data uploads
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Release Notes for 2.0.7:
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------------------------
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This is a patch release for Metacat replication
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* Replication SQL performance enhancement
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* Comply with DataONE schema for SystemMetadata.submitter
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Release Notes for 2.0.6:
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------------------------
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This patch release focuses on Metacat support for DataONE-enabled Morpho clients
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* MN.generateIdentifier() support for UUID and DOI
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* DOI registration support using EZID service
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* Pathquery support for specifying multiple document owners
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Release Notes for 2.0.5:
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------------------------
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This patch release focuses on Metacat support for Oracle
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*SystemMetadata table names have been shortened to comply with Oracle limits.
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*SANParks/SAEON spatial zip file download fixed
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*Pathquery performance fix
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*Hazelcast 2.x upgrade
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*Correct handling for deleted and archived objects for both Metacat and DataONE APIs
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Release Notes for 2.0.4:
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------------------------
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This patch release focuses on Metacat-Metacat replication.
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*Allows Metacat to stream replication update information between servers to avoid connection timeout issues
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*Allows Metacat replication when source host does not provide SystemMetadata (DataONE)
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*Fixes an access control issue that could allow search results to include protected documents
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Release Notes for 2.0.3:
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------------------------
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This is another critical patch release of Metacat 2.0.
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*Addresses a bug that prevented Metacat replication from completing (timeout error)
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*Uses more efficient SystemMetadata synchronization using shared Hazelcast map
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Release Notes for 2.0.2:
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------------------------
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This is a critical patch release of Metacat 2.0.
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*Addresses a bug that prevented updates to DataONE identified datapackages (e.g., using DOIs)
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*Addresses a bug that prevented the use of the Metacat API 'getaccesscontrol' action
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*Updates the Foresite ORE library to correctly serialize resource map documents
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Release Notes for 2.0.1:
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------------------------
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This is a minor patch release of Metacat 2.0. Please see the previous release notes for complete information.
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*Addresses an identifier issue during ORE generation for DataONE services
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*Increases compatibility with older EML content and the Xalan XSLT processor
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*Removes XSLT 2.0 support (Saxon)
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Release Notes for 2.0.0:
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------------------------
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This major release includes support for DataONE.
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*The DataONE v1.0.0 Member Node service APIs are now the preferred method for communicating with Metacat
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*The existing EcoGrid and Metacat Servlet APIs are deprecated but still available.
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*EML-embedded access control rules using permOrder="denyFirst" are no longer supported (https://redmine.dataone.org/issues/2614) 
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*Replication now utilizes client certificates to establish SSL connections between replication source and target servers
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*Access control rules now apply to objects on a per-revision basis rather than per-docid
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*Bugs fixed include:
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-SANParks skin/TPC (5561, 5530, 5533, 5542, 5543, 5544, 5551, 5563, 5566, 5567, 5569, 5353)
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-Registry (5114, 5244)
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-Replication (4907, 5537, 5536, 5534, 5520, 5519, 3296)
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-Spatial cache regeneration can be skipped during reconfiguration/redeployment/upgrade (3811)
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-Pathquery support for temporal search criteria (2084)
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-Character encoding of XML now respected (internationalization) (2495, 4083, 3815)
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Release Notes for 1.9.5:
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------------------------
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This release fixes those bugs:
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*Metacat could not download the included schemas in an external schema file during inserting.
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*Workflow scheduler could not work since the metadata standard of kepler kar file was changed. 
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*Earthgrid could not transform the Earthgrid query with concept "/" to the Metacat path query correctly.
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*Document access rules are now preserved when documents are archived during the 'delete' action.
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Release Notes for 1.9.4:
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------------------------
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This release fixes bugs in the FGDC data package upload and download interface utilized
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by the SANParks and SAEON skins.
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Release Notes for 1.9.3:
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------------------------
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This release fixes a harvester bug that prevented the EML harvester from processing
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harvest lists.
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The Kepler skin has been updated to support KarXML 2.1.
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Ecogrid query services now support multiple namespace searches.
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Release Notes for 1.9.2:
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------------------------
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This release primarily holds the addition of the Threshold of Potential
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Concern workflow functionality (TPC).  The following issues were addressed:
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* Create a properties file for use by JUnit Tests (Bug 2994)
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* security issue with skins (Bug 3368)
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* reorganize classes into a more functional specific structure (Bug 3510)
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* Add admin names as dropdown in configuration login (Bug 3729)
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* KNB metacat replication error log file is empty (Bug 3885)
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* Create TPC Report web browse/search pages (Bug 4165)
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* Create archive extraction functionality (Bug 4166)
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* Create Workflow Scheduler (Bug 4167)
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* metacat didn't update xml_path_index table while a document was updated (Bug 4367)
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* Enforce permissions for tpc workflow viewing and scheduling (Bug 4420)
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* Fix cross platform TPC GUI issues (Bug 4556)
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* TPC Sanparks page content lenth issue (Bug 4557)
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* Create validate and isAuthorized unit tests (Bug 4558)
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* Cannot insert replication server via gui (Bug 4594)
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* Timed Replication takes many hours and drives the load up on KNB (Bug 4616)
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* [ESA] Update fails when document rev number is missing (Bug 4627)
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* fails to catch some insert and update failures (Bug 4637)
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* must support java 1.6 (Bug 4641)
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* Convert build to pull eml from svn instead of cvs (Bug 4644)
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* handleGetRevisionAndDocTypeAction should search both xml_documents and xml_revisions table (Bug 4645)
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* Metacat couldn't update a document from client, which previous versions only stay in xml_revisions table (Bug 4649)
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* metacat runs out of memory (Bug 4658)
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* ESA skin links are hard coded to data.esa.org (Bug 4698)
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* Update release 1.9.2 release notes (Bug 4707)
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* Handle writing a text node > 4000 characters to the db. (Bug 4708)
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* Metacat should run against Tomcat 6 (Bug 4716)
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Release Notes for 1.9.1:
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------------------------
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The 1.9.1 release holds the bug fixes found after releasing 1.9.0 beta.  
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These bugs were primarily replication issues.  There is no difference 
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in functionality between 1.9.0 and 1.9.1 
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Release Notes for 1.9.0:
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------------------------
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This release focuses on simplifying the Metacat installation process by 
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creating a binary (war) installation.  The need to build the application
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on the server has been removed (although the option is still available).
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In order to facilitate this method of installation, a few major modifications
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were made to the code:
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  -- Ant token replacement was removed for all non-build variables in the 
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     application (most of this was already done in 1.8.1).
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  -- The Metacat properties confguration was moved into the application
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     itself.
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  -- Database schema version detection and install/upgrade utilities were 
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     added to the application.
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Also, this release includes several enhancements:
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  -- it supports the new EML 2.1.0 version.  
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  -- Documents are now stored on the local filesystem as well as in the 
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     database in order to preserve document integrity.
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  -- Metacat verifies new schemas when they are added.
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  -- Additional access is propegated with documents during replication.
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High priority bugs were addressed in this release as well.
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The enhancements/bugs addressed are:
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* escaped "less than" in inlinedata causes invalid eml output (Bug 2564)
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* need to set filename for download files (Bug 2566)
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* add ability for search engines to index metacat documents (Bug 2826)
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* EML citation section should include both organizationNames and individualNames (Bug 3059)
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* refactor skins to get organization list from metacat getOrganizations() function (Bug 3114)
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* Update dataknp.sanparks.org packageId attributes to match Metacat Ids (Bug 3258)
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* New documents explicitly set as public access don't show up correctly (Bug 3262)
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* Modify confguration utility in metacat (Bug 3371)
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* Integrate perl token replacement changes (Bug 3372)
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* Create skin specific configuration utility (Bug 3373)
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* Add authentication for configuration utility (Bug 3374)
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* Create a sorted properties utility (Bug 3375)
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* Add DB upgrade/install functionality to java code (Bug 3376)
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* Create ANT install target for developers (Bug 3377)
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* Create LSID server installation (Bug 3380)
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* Create unit test code for 1.9 additions (Bug 3381)
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* create simple turnkey installer for metacat Phase I (Bug 3461)
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* Maps do not display in Firefox version 3 (Bug 3462)
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* Replicate access rules in replication (Bug 3464)
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* Metacat casesensitive="true" option in pathquery expressions is broken (Bug 3472)
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* Add full schema checking when metacat register new schema (Bug 3474)
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* Incorporate EML 2.1.0 access changes in metacat (Bug 3495)
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* getprincipals action returns invalid XML document (Bug 3527)
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* Update knbweb to serve new metacat install (Bug 3545)
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* Replication should write to disk (Bug 3554)
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* Update acknowlegements in metacat readme (Bug 3588)
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* Validate the ldap administrator field. (Bug 3616)
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* Allow for different authentication services in metacat configuration (Bug 3680)
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* Tag utilities module and have metacat check out that tag (Bug 3685)
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Release Notes for 1.8.1:
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------------------------
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This release focuses on bug fixes. In this release, the problem that Metacat 1.8.0 and previous 
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versions use illegitimate EML 2.0.1 schemas is addressed: first, Metacat 1.8.1 comes with
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legitimate EML 2.0.1 schemas; second, existing invalid EML 2.0.1 documents will be 
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automatically fixed while maintaining their package ID during the Metacat 1.8.1 upgrading process. 
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Details please see:
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http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3239
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http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3241
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Note: after upgrading the Metacat to version 1.8.1, some replication issues may be seen, e.g., the 
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EML 2.0.1 documents from Metacat 1.8.0 or ealier verions may be rejected since Metacat 1.8.1 uses
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different EML 2.0.1 schemas (see bug 3239). If this is case, Metacat administrators should notify
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their counterparts to upgrade previous version Metacats to 1.8.1. 
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The fixed bugs include:
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*Character set (charset) problem when filling out form (Bug2797)
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*Charset bug: > "less than" symbol does not display correctly (Bug2517)
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*Metacat performance issue in Sanparks skin (Bug 3174)
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*Metacat using illegitimate versions of EML schema (Bug 3239)
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*Update older invalidated eml201 document in Metacat (Bug 3241)
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*Verify existing token changes to skins (Bug 3176)
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*The edit feature in the NCEAS Data Repoistory does not work (Bug 2644)
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*Expose permission options for registry uploads (Bug 3014)
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*ESA registry doesn't have LTER in login dropdown menu (Bug 2647)
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*Data Catalog Map is slow when selecting (Bug2732)
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*Only one attribute per element returned with pathquery results(Bug 2999)
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*The field "skinconfigs" in the MetacatUtil class is public (Bug 3057)
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*Generalize the reading of skin.configs in DBTransform (Bug3058)
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*The query example in metacatquery.html document need to be changed (Bug3137)
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*Add upload method into Metacat tour (Bug 3139)
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*Query resultset doesn't show component name in kepler skin (Bug 3178)
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*Add fields used in Morpho search to the default indexPaths property (Bug 3259)
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*Private data cannot be downloaded from metadata display page (xsl) (Bug 3263)
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*An error message happen during the metacat start up (Bug 3279)
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*Replication: Timed replication failures occur twice instead of once (Bug 3304)
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*Inline Data does not work correctly without the <pre> tag (Bug 3088)
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*Include FGDC metadata in KNB and NCEAS skin search results (Bug 3146)
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Release Notes for 1.8.0:
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------------------------
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This release focuses on improving query performance.  Both the selection 
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and access control queries were rewritten to execute efficiently.
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To improve search performance, a query caching mechanism was introduced. 
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Cached queries are currently supported only for public users.
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New Features:
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* Data registries now support uploading of data objects along with data 
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  packages (Bug 1982)
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Bug Fixes:
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* Metacat Performace: Rewrite the xml_nodes queries (Bug 2155)
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* Metacat Performace: Rewrite the xml_access part of the query (Bug 2557)
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* Query cache mechanism (Bug 2905)
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* Metacat Performance: updates from Morpho of data packages are taking 
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   longer than five minutes (Bug 2805)
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* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
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* Metacat Performace: Upgrading hardware setup (Bug 2175)
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* Metacat Performace: Add/drop indices on key columns (Bug 2153)
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* Display of metadata documents reorganized, including a new citation format,
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  obvious download options, and a redesigned data table layout (Bugs 2981, 2832)
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* I.E. display fixes on default skin (Bug 2579)
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* Web Address links fixed (Bug 2147)
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* NCEAS skin redesigned to use IFRAME-less layout, match new website.
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* Spatial query:  data packages must be fully contained by the selection 
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  bounding box in order to appear in the search results (Bugs 2972, 2732).
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* FGDC support: upload, delete, update, access control, and download
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  (Bugs 2807, 2925, 2926, 2929, 2030).
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Compatibility Notices:
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* Tomcat 3 and 4 are no longer tested or supported. Users are 
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  highly encouraged to upgrade to Tomcat 5.5
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Release Notes for 1.7.0:
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------------------------
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This release features only a few minor changes to the core Metacat engine. 
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The major focus of this release is the addition of the spatial functionality.
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The geographic coverage of metadata documents can now be cached in a GIS-
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accessible format and published via web mapping services and an online
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interactive map. 
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New Features:
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* Three new open source libraries have been integrated with Metacat:
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  - Geoserver:  A standards-compliant web map server to publish
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                geographic data to the web.
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               (http://docs.codehaus.org/display/GEOS/Home)
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  - GeoTools:   A java-based GIS toolkit to programatically
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                manipulate spatial datasets.
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                (http://geotools.codehaus.org/)
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  - Mapbuilder: A javascript application to provide an interactive
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                web map front-end to Geoserver.
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                (http://docs.codehaus.org/display/MAP/Home)
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* Spatial Caching/Indexing mechanism; documents with geographic
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  coverages will be added to the spatial cache.
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* Spatial Query action in metacat servlet. 
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* Interactive Web map to visualize and query the spatial 
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  distribution of metadata documents.
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* Experimental python, ruby and php client libraries to interface with metacat.
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* Preliminary process in place for web based configuration of metacat.
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Compatibility Notices:
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* Tomcat 3 and 4 are no longer tested or supported. Users are 
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  highly encouraged to upgrade to Tomcat 5.5
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392
Bug Fixes:
393
* Metacat administrators are able to modify and delete documents 
394
  created by other users.
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* Fixed problems with indexing XML attributes, see bug 2469
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Release Notes for 1.6.0:
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------------------------
400

    
401
This release comes with more performance improvements, initial support for 
402
LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for 
403
Metacat administrators and bug fixes. Below is the list of bug fixes and
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performance improvements.
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406
Bug Fixes: 
407
* Improved the indexing algorithm. Earlier indexing failed for some documents 
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  randomly and used to take a lot of time to complete for others. The 
409
  code for indexing was changed to take care of both these problems.
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* Earlier, xmlns prefix was used to determine the namespace of the document. 
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  Now schemaLocation is used instead xmlns prefix to determine the namespace 
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  of the document as that is a better indicator of document type. 
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* INSTR was used in some SQL statements and it is not supported by Postgres. 
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  So SQL statements were modified so that INSTR is not used.
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* Replication was changed to include replication of deleted documents also.
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* Fixed bug in squery which didnt allow use of not-contains 
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New Features:
419
* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
420
* Added support for LSID. This includes modifying the stylesheets to 
421
  display the LSIDs, modifying the build to include a new target 
422
  'install-ldap'.
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* Added following access control levels to Metacat:
424
    1. Administrators - users who can do the following:
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       a. Run replication
426
       b. Delete any document
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       c. Modify any document
428
       d. run indexing for any document
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       e. check the logs
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    2. allowedUsers - User who are allowed to submit
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    3. deniedUsers - Users not allowed to submit
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* Added a new skin for Ecological Society of America. 
433
* Created an Advanced search servlet which can be used from the web. 
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* Various connections have been modified to be secure. e.g. connection between 
435
ldaps is made secure now, replication is done over secure channels.  
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437
Performance:
438
* Reduced size of xml_nodes by creating a new table for holding nodes from 
439
  deleted documents and old revisions of the documents. 
440
* Provided a new variable in metacat.properties where more frequently searched 
441
  for paths can be specified. Seperate indexes are created for these paths 
442
  - so that search is faster.
443
* Included log4j for logging and debuging to prevent wasting of time in printing log statements. 
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Release Notes for 1.5.0:
446
------------------------
447

    
448
This release comes with performace improvement, user interface enhancements,
449
and bug fixes. Below is the list of bug fixes and performance improvements. 
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451
Bug Fixes:
452
* Modify property values of harvester registration servlets to match the
453
  servlet-mapping URL values in web.xml. The old values used the servlet
454
  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
455
  Windows. The new values use the servlet-mapping URL values. This should
456
  work in both Tomcat 4 and Tomcat 5. (Bug 162)
457
* Re-implement logic to prune old log entries from the HARVEST_LOG and
458
  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
459
  violations in the database because it tried to delete parent records from
460
  HARVEST_LOG prior to deleting child records from
461
  HARVEST_DETAIL_LOG. (Bug 162)
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* In data registry, minor bugs fixed like the error page shows the link back
463
  to the form when error page was generated because of a document read
464
  request from search results page,  the successful delete button leading
465
  to a blank screen and the old ACL overwritten by the registry.
466
  (Bugs 1307, 1310, 1322, 1344, 1551)
467
* Changed the code to support insertion of following characters: ', `,
468
  charcters in the Numeric Character Reference format (&#xyz;) and
469
  characters like µ. Characters like µ will be converted to and stored in
470
  Numeric Character Reference format(&#xyz;). They will also be returned
471
  in Numeric Character Reference and it is upto the client to convert them
472
  and display them accordingly in the application. Partial fix provided by
473
  Johnoel Ancheta. (Bug 1538,1711)
474
* Spatial search failed on Oracle because of invalid entries made by
475
  some documents in the nodedata column of xml_nodes for paths involving
476
  'eastBoundingCoordinate', 'westBoundingCoordinate',
477
  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
478
  nodedatanumerical was added to xml_nodes table such that all the numerical
479
  nodedata is stored in this column and this column is now used for spatial
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  search. (Bug 1703, 1718)
481
* In the default skin, clicking on the keywords on the home page did not
482
  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
483
* Metacat generated a success message even when a document which didnt
484
  exsist was requested for deletion. This has been fixed. (Bug 1850)
485
* "packagetype" in xml-relation table was entered as eml200 namespace when
486
  an eml201 document was inserted. This is fixed now so that "packagetype"
487
  in xml-relation table points to eml201 namespace. (Bug 1979)
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* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
489
  earlier. Fixed such that it points to the locally installed metacat url. 
490
  (Bug 1986)
491
* Changes to the Query subsystem fix bugs that prevented attributes from 
492
  being expressed solely in the xpath query statement and the returnfield 
493
  values. For instance, a query URL may now include search strings like 
494
  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
495
  Previously, the attribute had to be appended to an element: 
496
  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
497
  QuerySpecification.java, and QueryTerm.java (Bug 2052)
498
* Search query failed in case of Oracle if number of documents in the result
499
  were more than 1000. This has been fixed. (Bug 2000)
500
* Removed any occurence of enum which is now a keyword in Java 1.5
501

    
502

    
503
Enhancements:
504
* Major improvements done in user interface for the data registeries and
505
  various other skins. Improvements done based on suggestions from Mark
506
  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
507
  the default skin and ldap templates. (Bug 1948)
508
* Coded added such that administrator can delete documents irrespective of
509
  who the document belongs to.
510
* Performance impovement done in searching of datasets. A part of the search
511
  time was taken up because of generation of resultset after the search had be
512
  done. So this was the sequence of events in earlier metacat
513
  1) Search for the given text
514
  2) A list of docids generated
515
  3) For each of the docids
516
     3a) Use xml_index and xml_nodes table to generate the string descibing
517
         the document including the returnfields requested in the search
518
  4) Add all the strings from step 3a to send back the resultant
519
     document. Here a decent amount of time was being taken by step 3a. 
520
  The algorithm is now modified by addition of two tables xml_queryresult and
521
  xml_returnfields and a user defined parameter xml_returnfield_count. The
522
  new algorithm works as follows:
523
  1) Search for the given text
524
  2) A list of docids is generated
525
  3) For the given set of return fields generate a unique string and check
526
     if that string exists in xml_returnfields
527
     3a) If string does not exist in xml_returnfield, then enter a new
528
         record usage_count as 1 and returnfield_string as the unique string
529
         generated above.
530
     3b) Else if the string exists, increment usage_count
531
  4) Given the docids from step 2 and the id of the returnfield record from
532
     step 3, query for any docids that already exist in xml_queryresult.
533
     For the docids that do exist, get the queryresult_string.
534
  5) For rest of the docids from step2 which were not found in step 4, do
535
     the following for each of the documents:
536
     5a) Use xml_index and xml_nodes table to generate the string descibing
537
         the document including the returnfields requested in the search
538
     5b) If usage_count of the record from step is more than
539
         xml_returnfield_count set in metacat.properties, then store the
540
         string in xml_queryresult as a record which has the returnfield_id
541
         representing the set of returnfields, docid representing the
542
         document and the string as queryresult_string.
543
  6) Add all the strings from step 4 and step 5a to send back the resultant
544
     document
545
  So the results from step 3a in previous algorithm are effectively cached
546
  and hence same computation is not done again and again for each search.
547
  When a document is deleted, all the entries for that document in
548
  xml_queryresult table are also deleted. When a document is updated, all
549
  the entries for that document in xml_queryresult table are deleted. This
550
  works fine because those entries will be generated and cached again the
551
  next time the document is part of a search is requested.
552
* Performance impovement done for % search.
553
* Following new functions added to metacat client API: a method to set access
554
  on an xml document and a method to get newest version for a given document.
555
* Implement a new HarvesterServlet for running Harvester as a servlet. This
556
  eliminates the need to run Harvester in a terminal window. By default, the
557
  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
558
  documentation will be modified to instruct Harvester administrators to
559
  uncomment the HarvesterServlet entry.
560
* Minor enhancement to support multiple email addresses for harvester
561
  administrator and site contact. Each address is separated by a comma or
562
  semicolon.
563
* Increase number of rows in Harvest List Editor from 300 to 1200.
564
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
565
  value when it is set to 0 or a negative number. This allows Harvester to
566
  run indefinitely without shutting down after reaching a maximum number of
567
  harvests. The previous default value of 30 would cause Harvester to
568
  terminate after 30 harvests.
569

    
570
Details of all changes can be found in the bug database here:
571
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
572

    
573

    
574
Release Notes for 1.4.0:
575
------------------------
576

    
577
This is a major release, and is the first to introduce many new features to
578
Metacat.  Some of the major new features in this version of Metacat include:
579

    
580
* Added a new 'Harvester' that allows documents to be periodically pulled
581
  from distributed sources into metacat, useful for interfacing with other
582
  system types. See the Metacat Tour for details.
583
* Added new 'skins' capability to allow the GUI for the metacat web interface
584
  to be more easily customized to fit into site needs.  The skin is based on
585
  a flexible mix of XSLT, CSS, and Javascript.
586
* Added a web-based metadata entry form for submitting limited EML documents
587
  as part of a data registry.  The GUI for the registry is customizable and 
588
  is integrated with the 'skins' system for the main metacat interface.  The
589
  registry subsystem is written in Perl, and can simultaneously be used to 
590
  present multiple 'registry' interfaces.
591
* A new 'client API' has been developed and implemented in Java and in Perl 
592
  so that metacat functions can be accessed from any program in those
593
  languages.  The client API supports the major metacat servlet actions,
594
  including login(), logout(), query(), insert(), update(), delete(), and 
595
  upload(). See the Metacat Tour for details.
596
* Added a new 'getlog' action that produces a usage history for all major
597
  events.  So now an XML report can be generated for document reads, inserts,
598
  deletes, etc.  See the new section in the Metacat Tour.
599
* Added a new 'buildindex' action that can rebuild the index entries for any
600
  document in the database.
601
* The configuration file for metacat (metacat.properties) has been moved out
602
  of the jar file and into the WEB-INF directory, allowing far easier changes
603
  to the configuration parameters.
604
* Results in default web interface are sorted by title in the XSLT 
605
  (configurable)
606
* Many bugs were fixed.
607

    
608
Details of all changes can be found in the bug database here:
609
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
610

    
611
Release Notes for 1.3.1:
612
------------------------
613

    
614
This is a simple interim bug fix. No major functionality changes. Bugs fixed 
615
include:
616
 1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in 
617
    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3 
618
    and Java 1.4.
619
 2) Distribution package size was reduced.
620

    
621

    
622
Release Notes for 1.3.0
623
------------------------
624

    
625
In 1.3.0 release, the structure of the xml_access table was changed and a new
626
table, xml_accesssubtree was added. If you try to update a previously 
627
installed Metacat, you should run a script file to updated the table structure 
628
before installation.
629
For Oracle user: At the SQLPLUS prompt type the following -
630
@src/reviseformetacat13.sql
631
For Postgresql user: At install directory prompt type the following -
632
psql exp < src/reviseformetacat13_postgres.sql
633
(where 'exp' is the database name).
634

    
635
After installation, user should run "ant schemasql" command to register EML2
636
schema in xml_catalog table.
637

    
638
If you are a new Metacat user, this step is unneeded.
639

    
640
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise, 
641
         it will cause potential replication issues.
642
      2) Delete the xercesImpl.jar and xmlParserAPIs.jar files 
643
         which are in $CATALINA_HOME/common/endorsed. They are old version and
644
         don't support XML schema validation.
645

    
646
New Features in 1.3.0
647
  1) Partialy support EML2 document. User can store, query, read and write
648
     EML2 documents. However, Metacat only support access control in resource
649
     level. The subtree level access control will be ignored.
650
  2) Support other xml document base on namespace/schema.
651
  3) Support query for attribute value
652
  4) Assign MIME type to data file base on metadata when user try to read it.
653
  5) Owner can assign access rules to a document which does not have access 
654
     document to apply it.
655
  6) Support exporting single file, not only whole package
656
  7) Resupport Microsoft SQL Server.
657

    
658
Fixes in 1.3.0:
659
  1) Couldn't finish delta T replication for large set of documents.
660
  2) Couldn't create access control during delta T replication.
661
  3) Eorr will be written to a seperated log file if some documents
662
     were failed in replication.
663
  4) Decrease the time to create access rules during insert or update 
664
     a package.
665
     
666
Documentation
667
-------------
668
See the docs directory for detailed documentation and installation
669
instructions.
670

    
671
Details of the Metacat architecture can be found on the website for
672
the Knowledge Network for Biocomplexity (KNB):
673

    
674
  http://knb.ecoinformatics.org/software/metacat/
675

    
676
Contributions to this work are welcome.  Please see the above web site
677
for details on how to contribute.
678

    
679
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
680
-----------------------------------------------------------------------------
681
If you discover a bug please report it, either by email (above) or by using
682
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
683
list of currently unimplemented features in Bugzilla that we are working on
684
for the next release.
685

    
686
Legalese
687
--------
688
This software is copyrighted by The Regents of the University of California
689
and the National Center for Ecological Analysis and Synthesis
690
and licensed under the GNU GPL; see the 'LICENSE' file for
691
details.
692

    
693
This material is based upon work supported by the
694
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
695
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations 
696
expressed in this material are those of the author(s) and do not necessarily 
697
reflect the views of the National Science Foundation (NSF).
698

    
699
This software is partially supported by a grant from the Andrew W. 
700
Mellon Foundation.
701

    
702
This product includes software developed by the Apache Software
703
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
704
for details.
705

    
706
The source code, object code, and documentation in the com.oreilly.servlet
707
package is copyright and owned by Jason Hunter. See the cos-license.html file
708
for details of the license.  Licensor retains title to and ownership of the
709
Software and all enhancements, modifications, and updates to the Software.
710

    
711
This software includes the JDBC driver for PostgreSQL.  See the 
712
postgresql-license.txt file for details.