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#
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# '$RCSfile$'
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# '$Author$'
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# '$Revision$'
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# '$Date$'
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#
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2479
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Metacat: XML Metadata and Data Management System
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------------------------------------------------
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666
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jones
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3611
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tao
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Version: 1.8 Release
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666
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jones
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1295
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jones
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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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696
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jones
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666
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jones
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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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981
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tao
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Jing Tao (tao@nceas.ucsb.edu)
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666
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jones
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Jivka Bojilova (bojilova@nceas.ucsb.edu)
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20 |
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Dan Higgins (higgins@nceas.ucsb.edu)
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2313
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jones
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Saurabh Garg (sgarg@nceas.ucsb.edu)
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Duane Costa (dcosta@lternet.edu)
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2480
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jones
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Veronique Connolly (connolly@nceas.ucsb.edu)
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2905
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harris
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John Harris (harris@nceas.ucsb.edu)
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25 |
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Callie Bowdish (bowdish@ecoinformatics.org)
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Will Tyburczy (tyburczy@ecoinformatics.org)
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3020
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sgarg
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Matthew Perry (perry@nceas.ucsb.edu)
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3130
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perry
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Chad Burt (underbluewaters@gmail.com)
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3612
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walbridge
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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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2480
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Patch contributors:
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Andrea Chadden (chadden@nceas.ucsb.edu)
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2479
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jones
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Chris Jones (cjones@msi.ucsb.edu)
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2480
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jones
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Johnoel Ancheta (johnoel@hawaii.edu)
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Owen Jones (owen.jones@imperial.ac.uk)
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1311
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berkley
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982
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berkley
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Metacat is a flexible database storage system for XML formatted
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2313
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jones
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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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2441
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jones
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storage, retrieval, query, validation, and transformation (using the XSLT
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2313
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jones
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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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666
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Installation
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------------
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See the file "docs/user/metacatinstall.html" for detailed instructions.
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3611
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tao
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Release Notes for 1.8:
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3376
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tao
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------------------------
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3612
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walbridge
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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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3376
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tao
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3612
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walbridge
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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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3376
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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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3613
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leinfelder
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* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
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3376
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tao
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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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3612
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walbridge
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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 (Bug 2832)
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* NCEAS skin redesigned to use IFRAME-less layout, match new website.
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3613
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leinfelder
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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 (Bug 2972).
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3376
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tao
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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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3109
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perry
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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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3020
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sgarg
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perry
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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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3135
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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
|
114 |
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|
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Bug Fixes:
|
116 |
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* Metacat administrators are able to modify and delete documents
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created by other users.
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3153
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jones
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* Fixed problems with indexing XML attributes, see bug 2469
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119 |
3109
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perry
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|
120 |
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121 |
3020
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sgarg
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Release Notes for 1.6.0:
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------------------------
|
123 |
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|
124 |
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This release comes with more performance improvements, initial support for
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125 |
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LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for
|
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Metacat administrators and bug fixes. Below is the list of bug fixes and
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performance improvements.
|
128 |
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|
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Bug Fixes:
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* 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
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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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3025
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sgarg
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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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3020
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sgarg
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New Features:
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* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
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* Added support for LSID. This includes modifying the stylesheets to
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144 |
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display the LSIDs, modifying the build to include a new target
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'install-ldap'.
|
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* Added following access control levels to Metacat:
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1. Administrators - users who can do the following:
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a. Run replication
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b. Delete any document
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c. Modify any document
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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.
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3025
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sgarg
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* Created an Advanced search servlet which can be used from the web.
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157 |
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* Various connections have been modified to be secure. e.g. connection between
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ldaps is made secure now, replication is done over secure channels.
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3020
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sgarg
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Performance:
|
161 |
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* Reduced size of xml_nodes by creating a new table for holding nodes from
|
162 |
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deleted documents and old revisions of the documents.
|
163 |
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* Provided a new variable in metacat.properties where more frequently searched
|
164 |
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for paths can be specified. Seperate indexes are created for these paths
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165 |
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- so that search is faster.
|
166 |
3025
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sgarg
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* Included log4j for logging and debuging to prevent wasting of time in printing log statements.
|
167 |
3020
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sgarg
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|
168 |
2475
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sgarg
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Release Notes for 1.5.0:
|
169 |
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------------------------
|
170 |
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|
171 |
2479
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jones
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This release comes with performace improvement, user interface enhancements,
|
172 |
2475
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sgarg
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and bug fixes. Below is the list of bug fixes and performance improvements.
|
173 |
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|
174 |
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Bug Fixes:
|
175 |
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* Modify property values of harvester registration servlets to match the
|
176 |
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servlet-mapping URL values in web.xml. The old values used the servlet
|
177 |
|
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class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
|
178 |
|
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Windows. The new values use the servlet-mapping URL values. This should
|
179 |
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work in both Tomcat 4 and Tomcat 5. (Bug 162)
|
180 |
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* Re-implement logic to prune old log entries from the HARVEST_LOG and
|
181 |
|
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HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
|
182 |
|
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violations in the database because it tried to delete parent records from
|
183 |
|
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HARVEST_LOG prior to deleting child records from
|
184 |
|
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HARVEST_DETAIL_LOG. (Bug 162)
|
185 |
|
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* In data registry, minor bugs fixed like the error page shows the link back
|
186 |
|
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to the form when error page was generated because of a document read
|
187 |
|
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request from search results page, the successful delete button leading
|
188 |
|
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to a blank screen and the old ACL overwritten by the registry.
|
189 |
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(Bugs 1307, 1310, 1322, 1344, 1551)
|
190 |
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* Changed the code to support insertion of following characters: ', `,
|
191 |
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charcters in the Numeric Character Reference format (&#xyz;) and
|
192 |
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characters like µ. Characters like µ will be converted to and stored in
|
193 |
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Numeric Character Reference format(&#xyz;). They will also be returned
|
194 |
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in Numeric Character Reference and it is upto the client to convert them
|
195 |
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and display them accordingly in the application. Partial fix provided by
|
196 |
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Johnoel Ancheta. (Bug 1538,1711)
|
197 |
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* Spatial search failed on Oracle because of invalid entries made by
|
198 |
|
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some documents in the nodedata column of xml_nodes for paths involving
|
199 |
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'eastBoundingCoordinate', 'westBoundingCoordinate',
|
200 |
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'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
|
201 |
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nodedatanumerical was added to xml_nodes table such that all the numerical
|
202 |
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nodedata is stored in this column and this column is now used for spatial
|
203 |
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search. (Bug 1703, 1718)
|
204 |
|
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* In the default skin, clicking on the keywords on the home page did not
|
205 |
|
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result is a search being done. Fix provided by Owen Jones. (Bug 1768)
|
206 |
|
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* Metacat generated a success message even when a document which didnt
|
207 |
|
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exsist was requested for deletion. This has been fixed. (Bug 1850)
|
208 |
|
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* "packagetype" in xml-relation table was entered as eml200 namespace when
|
209 |
|
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an eml201 document was inserted. This is fixed now so that "packagetype"
|
210 |
|
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in xml-relation table points to eml201 namespace. (Bug 1979)
|
211 |
|
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* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
|
212 |
|
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earlier. Fixed such that it points to the locally installed metacat url.
|
213 |
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(Bug 1986)
|
214 |
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* Changes to the Query subsystem fix bugs that prevented attributes from
|
215 |
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being expressed solely in the xpath query statement and the returnfield
|
216 |
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values. For instance, a query URL may now include search strings like
|
217 |
|
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'@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
|
218 |
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Previously, the attribute had to be appended to an element:
|
219 |
|
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'/eml/@packageId=sbclter%25'. These fixes change DBQuery.java,
|
220 |
|
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QuerySpecification.java, and QueryTerm.java (Bug 2052)
|
221 |
|
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* Search query failed in case of Oracle if number of documents in the result
|
222 |
|
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were more than 1000. This has been fixed. (Bug 2000)
|
223 |
|
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* Removed any occurence of enum which is now a keyword in Java 1.5
|
224 |
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|
225 |
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|
226 |
|
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Enhancements:
|
227 |
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* Major improvements done in user interface for the data registeries and
|
228 |
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various other skins. Improvements done based on suggestions from Mark
|
229 |
|
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Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
|
230 |
|
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the default skin and ldap templates. (Bug 1948)
|
231 |
|
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* Coded added such that administrator can delete documents irrespective of
|
232 |
|
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who the document belongs to.
|
233 |
|
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* Performance impovement done in searching of datasets. A part of the search
|
234 |
|
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time was taken up because of generation of resultset after the search had be
|
235 |
|
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done. So this was the sequence of events in earlier metacat
|
236 |
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1) Search for the given text
|
237 |
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2) A list of docids generated
|
238 |
|
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3) For each of the docids
|
239 |
|
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3a) Use xml_index and xml_nodes table to generate the string descibing
|
240 |
|
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the document including the returnfields requested in the search
|
241 |
2479
|
jones
|
4) Add all the strings from step 3a to send back the resultant
|
242 |
|
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document. Here a decent amount of time was being taken by step 3a.
|
243 |
|
|
The algorithm is now modified by addition of two tables xml_queryresult and
|
244 |
|
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xml_returnfields and a user defined parameter xml_returnfield_count. The
|
245 |
|
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new algorithm works as follows:
|
246 |
2475
|
sgarg
|
1) Search for the given text
|
247 |
2479
|
jones
|
2) A list of docids is generated
|
248 |
2475
|
sgarg
|
3) For the given set of return fields generate a unique string and check
|
249 |
|
|
if that string exists in xml_returnfields
|
250 |
|
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3a) If string does not exist in xml_returnfield, then enter a new
|
251 |
|
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record usage_count as 1 and returnfield_string as the unique string
|
252 |
|
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generated above.
|
253 |
|
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3b) Else if the string exists, increment usage_count
|
254 |
|
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4) Given the docids from step 2 and the id of the returnfield record from
|
255 |
|
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step 3, query for any docids that already exist in xml_queryresult.
|
256 |
|
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For the docids that do exist, get the queryresult_string.
|
257 |
|
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5) For rest of the docids from step2 which were not found in step 4, do
|
258 |
|
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the following for each of the documents:
|
259 |
|
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5a) Use xml_index and xml_nodes table to generate the string descibing
|
260 |
|
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the document including the returnfields requested in the search
|
261 |
|
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5b) If usage_count of the record from step is more than
|
262 |
|
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xml_returnfield_count set in metacat.properties, then store the
|
263 |
|
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string in xml_queryresult as a record which has the returnfield_id
|
264 |
|
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representing the set of returnfields, docid representing the
|
265 |
|
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document and the string as queryresult_string.
|
266 |
|
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6) Add all the strings from step 4 and step 5a to send back the resultant
|
267 |
|
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document
|
268 |
|
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So the results from step 3a in previous algorithm are effectively cached
|
269 |
|
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and hence same computation is not done again and again for each search.
|
270 |
|
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When a document is deleted, all the entries for that document in
|
271 |
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xml_queryresult table are also deleted. When a document is updated, all
|
272 |
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the entries for that document in xml_queryresult table are deleted. This
|
273 |
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works fine because those entries will be generated and cached again the
|
274 |
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next time the document is part of a search is requested.
|
275 |
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* Performance impovement done for % search.
|
276 |
|
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* Following new functions added to metacat client API: a method to set access
|
277 |
|
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on an xml document and a method to get newest version for a given document.
|
278 |
|
|
* Implement a new HarvesterServlet for running Harvester as a servlet. This
|
279 |
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eliminates the need to run Harvester in a terminal window. By default, the
|
280 |
|
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HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
|
281 |
|
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documentation will be modified to instruct Harvester administrators to
|
282 |
|
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uncomment the HarvesterServlet entry.
|
283 |
|
|
* Minor enhancement to support multiple email addresses for harvester
|
284 |
|
|
administrator and site contact. Each address is separated by a comma or
|
285 |
|
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semicolon.
|
286 |
|
|
* Increase number of rows in Harvest List Editor from 300 to 1200.
|
287 |
|
|
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
|
288 |
|
|
value when it is set to 0 or a negative number. This allows Harvester to
|
289 |
|
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run indefinitely without shutting down after reaching a maximum number of
|
290 |
|
|
harvests. The previous default value of 30 would cause Harvester to
|
291 |
|
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terminate after 30 harvests.
|
292 |
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|
293 |
|
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Details of all changes can be found in the bug database here:
|
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http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
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Release Notes for 1.4.0:
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------------------------
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This is a major release, and is the first to introduce many new features to
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Metacat. Some of the major new features in this version of Metacat include:
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* Added a new 'Harvester' that allows documents to be periodically pulled
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from distributed sources into metacat, useful for interfacing with other
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system types. See the Metacat Tour for details.
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* Added new 'skins' capability to allow the GUI for the metacat web interface
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to be more easily customized to fit into site needs. The skin is based on
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a flexible mix of XSLT, CSS, and Javascript.
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jones
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* Added a web-based metadata entry form for submitting limited EML documents
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as part of a data registry. The GUI for the registry is customizable and
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is integrated with the 'skins' system for the main metacat interface. The
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registry subsystem is written in Perl, and can simultaneously be used to
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present multiple 'registry' interfaces.
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* A new 'client API' has been developed and implemented in Java and in Perl
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so that metacat functions can be accessed from any program in those
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languages. The client API supports the major metacat servlet actions,
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including login(), logout(), query(), insert(), update(), delete(), and
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upload(). See the Metacat Tour for details.
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* Added a new 'getlog' action that produces a usage history for all major
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events. So now an XML report can be generated for document reads, inserts,
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deletes, etc. See the new section in the Metacat Tour.
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* Added a new 'buildindex' action that can rebuild the index entries for any
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document in the database.
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* The configuration file for metacat (metacat.properties) has been moved out
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|
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of the jar file and into the WEB-INF directory, allowing far easier changes
|
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to the configuration parameters.
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jones
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* Results in default web interface are sorted by title in the XSLT
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(configurable)
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* Many bugs were fixed.
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jones
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Details of all changes can be found in the bug database here:
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http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
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|
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tao
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Release Notes for 1.3.1:
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jones
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------------------------
|
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1308
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tao
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|
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1775
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tao
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This is a simple interim bug fix. No major functionality changes. Bugs fixed
|
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include:
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1776
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tao
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1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in
|
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Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3
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and Java 1.4.
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tao
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2) Distribution package size was reduced.
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|
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|
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|
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Release Notes for 1.3.0
|
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jones
|
------------------------
|
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1775
|
tao
|
|
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|
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In 1.3.0 release, the structure of the xml_access table was changed and a new
|
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1628
|
tao
|
table, xml_accesssubtree was added. If you try to update a previously
|
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|
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installed Metacat, you should run a script file to updated the table structure
|
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|
|
before installation.
|
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|
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For Oracle user: At the SQLPLUS prompt type the following -
|
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|
|
@src/reviseformetacat13.sql
|
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|
|
For Postgresql user: At install directory prompt type the following -
|
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|
|
psql exp < src/reviseformetacat13_postgres.sql
|
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|
|
(where 'exp' is the database name).
|
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1334
|
tao
|
|
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1628
|
tao
|
After installation, user should run "ant schemasql" command to register EML2
|
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|
|
schema in xml_catalog table.
|
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|
|
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|
|
If you are a new Metacat user, this step is unneeded.
|
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|
|
|
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1769
|
tao
|
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise,
|
364 |
|
|
it will cause potential replication issues.
|
365 |
|
|
2) Delete the xercesImpl.jar and xmlParserAPIs.jar files
|
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|
|
which are in $CATALINA_HOME/common/endorsed. They are old version and
|
367 |
|
|
don't support XML schema validation.
|
368 |
|
|
|
369 |
1628
|
tao
|
New Features in 1.3.0
|
370 |
|
|
1) Partialy support EML2 document. User can store, query, read and write
|
371 |
|
|
EML2 documents. However, Metacat only support access control in resource
|
372 |
|
|
level. The subtree level access control will be ignored.
|
373 |
|
|
2) Support other xml document base on namespace/schema.
|
374 |
|
|
3) Support query for attribute value
|
375 |
|
|
4) Assign MIME type to data file base on metadata when user try to read it.
|
376 |
|
|
5) Owner can assign access rules to a document which does not have access
|
377 |
|
|
document to apply it.
|
378 |
|
|
6) Support exporting single file, not only whole package
|
379 |
1769
|
tao
|
7) Resupport Microsoft SQL Server.
|
380 |
1628
|
tao
|
|
381 |
|
|
Fixes in 1.3.0:
|
382 |
|
|
1) Couldn't finish delta T replication for large set of documents.
|
383 |
|
|
2) Couldn't create access control during delta T replication.
|
384 |
|
|
3) Eorr will be written to a seperated log file if some documents
|
385 |
|
|
were failed in replication.
|
386 |
|
|
4) Decrease the time to create access rules during insert or update
|
387 |
|
|
a package.
|
388 |
|
|
|
389 |
861
|
jones
|
Documentation
|
390 |
|
|
-------------
|
391 |
1311
|
berkley
|
See the docs directory for detailed documentation and installation
|
392 |
666
|
jones
|
instructions.
|
393 |
|
|
|
394 |
1311
|
berkley
|
Details of the Metacat architecture can be found on the website for
|
395 |
666
|
jones
|
the Knowledge Network for Biocomplexity (KNB):
|
396 |
|
|
|
397 |
805
|
jones
|
http://knb.ecoinformatics.org/software/metacat/
|
398 |
666
|
jones
|
|
399 |
|
|
Contributions to this work are welcome. Please see the above web site
|
400 |
|
|
for details on how to contribute.
|
401 |
|
|
|
402 |
848
|
jones
|
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
|
403 |
|
|
-----------------------------------------------------------------------------
|
404 |
2313
|
jones
|
If you discover a bug please report it, either by email (above) or by using
|
405 |
|
|
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
|
406 |
|
|
list of currently unimplemented features in Bugzilla that we are working on
|
407 |
|
|
for the next release.
|
408 |
805
|
jones
|
|
409 |
|
|
Legalese
|
410 |
|
|
--------
|
411 |
666
|
jones
|
This software is copyrighted by The Regents of the University of California
|
412 |
|
|
and the National Center for Ecological Analysis and Synthesis
|
413 |
|
|
and licensed under the GNU GPL; see the 'LICENSE' file for
|
414 |
|
|
details.
|
415 |
|
|
|
416 |
1311
|
berkley
|
This material is based upon work supported by the
|
417 |
2313
|
jones
|
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
|
418 |
2975
|
jones
|
0225676 for SEEK. Any opinions, findings and conclusions or recomendations
|
419 |
|
|
expressed in this material are those of the author(s) and do not necessarily
|
420 |
|
|
reflect the views of the National Science Foundation (NSF).
|
421 |
1307
|
jones
|
|
422 |
2505
|
sgarg
|
This software is partially supported by a grant from the Andrew W.
|
423 |
|
|
Mellon Foundation.
|
424 |
|
|
|
425 |
1311
|
berkley
|
This product includes software developed by the Apache Software
|
426 |
1307
|
jones
|
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
|
427 |
|
|
for details.
|
428 |
|
|
|
429 |
1311
|
berkley
|
The source code, object code, and documentation in the com.oreilly.servlet
|
430 |
1307
|
jones
|
package is copyright and owned by Jason Hunter. See the cos-license.html file
|
431 |
1311
|
berkley
|
for details of the license. Licensor retains title to and ownership of the
|
432 |
1307
|
jones
|
Software and all enhancements, modifications, and updates to the Software.
|
433 |
2441
|
jones
|
|
434 |
2599
|
jones
|
This software includes the JDBC driver for PostgreSQL. See the
|
435 |
|
|
postgresql-license.txt file for details.
|