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metacat / README @ 4627

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#
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#  '$RCSfile$'
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#   '$Author: daigle $'
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# '$Revision: 4622 $'
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#     '$Date: 2008-11-24 11:58:55 -0800 (Mon, 24 Nov 2008) $'
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#
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Metacat: XML Metadata and Data Management System
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------------------------------------------------
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Version: 1.9.0 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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              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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Patch contributors:
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              Andrea Chadden (chadden@nceas.ucsb.edu)
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              Chris Jones (cjones@msi.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/user/metacatinstall.html" for detailed instructions.
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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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Bug Fixes:
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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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* Fixed problems with indexing XML attributes, see bug 2469
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Release Notes for 1.6.0:
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------------------------
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This release comes with more performance improvements, initial support for 
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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.
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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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* 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:
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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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  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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* 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 
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ldaps is made secure now, replication is done over secure channels.  
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Performance:
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* Reduced size of xml_nodes by creating a new table for holding nodes from 
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  deleted documents and old revisions of the documents. 
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* Provided a new variable in metacat.properties where more frequently searched 
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  for paths can be specified. Seperate indexes are created for these paths 
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  - so that search is faster.
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* 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:
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------------------------
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This release comes with performace improvement, user interface enhancements,
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and bug fixes. Below is the list of bug fixes and performance improvements. 
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Bug Fixes:
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* Modify property values of harvester registration servlets to match the
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  servlet-mapping URL values in web.xml. The old values used the servlet
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  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
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  Windows. The new values use the servlet-mapping URL values. This should
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  work in both Tomcat 4 and Tomcat 5. (Bug 162)
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* Re-implement logic to prune old log entries from the HARVEST_LOG and
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  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
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  violations in the database because it tried to delete parent records from
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  HARVEST_LOG prior to deleting child records from
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  HARVEST_DETAIL_LOG. (Bug 162)
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* In data registry, minor bugs fixed like the error page shows the link back
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  to the form when error page was generated because of a document read
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  request from search results page,  the successful delete button leading
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  to a blank screen and the old ACL overwritten by the registry.
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  (Bugs 1307, 1310, 1322, 1344, 1551)
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* Changed the code to support insertion of following characters: ', `,
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  charcters in the Numeric Character Reference format (&#xyz;) and
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  characters like µ. Characters like µ will be converted to and stored in
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  Numeric Character Reference format(&#xyz;). They will also be returned
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  in Numeric Character Reference and it is upto the client to convert them
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  and display them accordingly in the application. Partial fix provided by
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  Johnoel Ancheta. (Bug 1538,1711)
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* Spatial search failed on Oracle because of invalid entries made by
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  some documents in the nodedata column of xml_nodes for paths involving
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  'eastBoundingCoordinate', 'westBoundingCoordinate',
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  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
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  nodedatanumerical was added to xml_nodes table such that all the numerical
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  nodedata is stored in this column and this column is now used for spatial
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  search. (Bug 1703, 1718)
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* In the default skin, clicking on the keywords on the home page did not
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  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
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* Metacat generated a success message even when a document which didnt
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  exsist was requested for deletion. This has been fixed. (Bug 1850)
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* "packagetype" in xml-relation table was entered as eml200 namespace when
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  an eml201 document was inserted. This is fixed now so that "packagetype"
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  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/
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  earlier. Fixed such that it points to the locally installed metacat url. 
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  (Bug 1986)
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* Changes to the Query subsystem fix bugs that prevented attributes from 
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  being expressed solely in the xpath query statement and the returnfield 
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  values. For instance, a query URL may now include search strings like 
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  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
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  Previously, the attribute had to be appended to an element: 
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  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
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  QuerySpecification.java, and QueryTerm.java (Bug 2052)
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* Search query failed in case of Oracle if number of documents in the result
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  were more than 1000. This has been fixed. (Bug 2000)
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* Removed any occurence of enum which is now a keyword in Java 1.5
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Enhancements:
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* Major improvements done in user interface for the data registeries and
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  various other skins. Improvements done based on suggestions from Mark
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  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
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  the default skin and ldap templates. (Bug 1948)
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* Coded added such that administrator can delete documents irrespective of
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  who the document belongs to.
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* Performance impovement done in searching of datasets. A part of the search
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  time was taken up because of generation of resultset after the search had be
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  done. So this was the sequence of events in earlier metacat
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  1) Search for the given text
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  2) A list of docids generated
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  3) For each of the docids
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     3a) Use xml_index and xml_nodes table to generate the string descibing
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         the document including the returnfields requested in the search
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  4) Add all the strings from step 3a to send back the resultant
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     document. Here a decent amount of time was being taken by step 3a. 
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  The algorithm is now modified by addition of two tables xml_queryresult and
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  xml_returnfields and a user defined parameter xml_returnfield_count. The
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  new algorithm works as follows:
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  1) Search for the given text
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  2) A list of docids is generated
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  3) For the given set of return fields generate a unique string and check
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     if that string exists in xml_returnfields
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     3a) If string does not exist in xml_returnfield, then enter a new
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         record usage_count as 1 and returnfield_string as the unique string
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         generated above.
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     3b) Else if the string exists, increment usage_count
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  4) Given the docids from step 2 and the id of the returnfield record from
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     step 3, query for any docids that already exist in xml_queryresult.
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     For the docids that do exist, get the queryresult_string.
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  5) For rest of the docids from step2 which were not found in step 4, do
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     the following for each of the documents:
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     5a) Use xml_index and xml_nodes table to generate the string descibing
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         the document including the returnfields requested in the search
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     5b) If usage_count of the record from step is more than
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         xml_returnfield_count set in metacat.properties, then store the
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         string in xml_queryresult as a record which has the returnfield_id
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         representing the set of returnfields, docid representing the
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         document and the string as queryresult_string.
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  6) Add all the strings from step 4 and step 5a to send back the resultant
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     document
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  So the results from step 3a in previous algorithm are effectively cached
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  and hence same computation is not done again and again for each search.
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  When a document is deleted, all the entries for that document in
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  xml_queryresult table are also deleted. When a document is updated, all
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  the entries for that document in xml_queryresult table are deleted. This
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  works fine because those entries will be generated and cached again the
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  next time the document is part of a search is requested.
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* Performance impovement done for % search.
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* Following new functions added to metacat client API: a method to set access
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  on an xml document and a method to get newest version for a given document.
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* Implement a new HarvesterServlet for running Harvester as a servlet. This
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  eliminates the need to run Harvester in a terminal window. By default, the
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  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
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  documentation will be modified to instruct Harvester administrators to
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  uncomment the HarvesterServlet entry.
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* Minor enhancement to support multiple email addresses for harvester
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  administrator and site contact. Each address is separated by a comma or
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  semicolon.
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* Increase number of rows in Harvest List Editor from 300 to 1200.
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* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
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  value when it is set to 0 or a negative number. This allows Harvester to
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  run indefinitely without shutting down after reaching a maximum number of
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  harvests. The previous default value of 30 would cause Harvester to
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  terminate after 30 harvests.
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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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* 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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  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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* 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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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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Release Notes for 1.3.1:
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------------------------
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This is a simple interim bug fix. No major functionality changes. Bugs fixed 
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include:
444
 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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 2) Distribution package size was reduced.
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Release Notes for 1.3.0
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------------------------
452

    
453
In 1.3.0 release, the structure of the xml_access table was changed and a new
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table, xml_accesssubtree was added. If you try to update a previously 
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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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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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After installation, user should run "ant schemasql" command to register EML2
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schema in xml_catalog table.
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If you are a new Metacat user, this step is unneeded.
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Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise, 
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         it will cause potential replication issues.
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      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
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         don't support XML schema validation.
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New Features in 1.3.0
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  1) Partialy support EML2 document. User can store, query, read and write
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     EML2 documents. However, Metacat only support access control in resource
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     level. The subtree level access control will be ignored.
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  2) Support other xml document base on namespace/schema.
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  3) Support query for attribute value
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  4) Assign MIME type to data file base on metadata when user try to read it.
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  5) Owner can assign access rules to a document which does not have access 
482
     document to apply it.
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  6) Support exporting single file, not only whole package
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  7) Resupport Microsoft SQL Server.
485

    
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Fixes in 1.3.0:
487
  1) Couldn't finish delta T replication for large set of documents.
488
  2) Couldn't create access control during delta T replication.
489
  3) Eorr will be written to a seperated log file if some documents
490
     were failed in replication.
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  4) Decrease the time to create access rules during insert or update 
492
     a package.
493
     
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Documentation
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-------------
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See the docs directory for detailed documentation and installation
497
instructions.
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Details of the Metacat architecture can be found on the website for
500
the Knowledge Network for Biocomplexity (KNB):
501

    
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  http://knb.ecoinformatics.org/software/metacat/
503

    
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Contributions to this work are welcome.  Please see the above web site
505
for details on how to contribute.
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Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
508
-----------------------------------------------------------------------------
509
If you discover a bug please report it, either by email (above) or by using
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our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
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list of currently unimplemented features in Bugzilla that we are working on
512
for the next release.
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Legalese
515
--------
516
This software is copyrighted by The Regents of the University of California
517
and the National Center for Ecological Analysis and Synthesis
518
and licensed under the GNU GPL; see the 'LICENSE' file for
519
details.
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This material is based upon work supported by the
522
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
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0225676 for SEEK.  Any opinions, findings and conclusions or recomendations 
524
expressed in this material are those of the author(s) and do not necessarily 
525
reflect the views of the National Science Foundation (NSF).
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This software is partially supported by a grant from the Andrew W. 
528
Mellon Foundation.
529

    
530
This product includes software developed by the Apache Software
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Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
532
for details.
533

    
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The source code, object code, and documentation in the com.oreilly.servlet
535
package is copyright and owned by Jason Hunter. See the cos-license.html file
536
for details of the license.  Licensor retains title to and ownership of the
537
Software and all enhancements, modifications, and updates to the Software.
538

    
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This software includes the JDBC driver for PostgreSQL.  See the 
540
postgresql-license.txt file for details.