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metacat / README @ 5192

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#
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#  '$RCSfile$'
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#   '$Author: daigle $'
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# '$Revision: 5192 $'
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#     '$Date: 2010-01-13 10:55:38 -0800 (Wed, 13 Jan 2010) $'
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Metacat: XML Metadata and Data Management System
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------------------------------------------------
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Version: 1.9.1 Release
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Send feedback and bugs to: metacat-dev@ecoinformatics.org
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                           http://bugzilla.ecoinformatics.org                         
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Version: 1.9.2 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/metacat-<OS>-install.html" for detailed instructions
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for your OS.
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Release Notes for 1.9.1:
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------------------------
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This release primarily holds the addition of the Threshold of Potential
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Concern workflow functionality (TPC).  
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 -- TPC workflow and workflow run pages added to SANParks skin.
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 -- Release supports running metacat on Java 1.6 JVM
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Release Notes for 1.9.1:
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------------------------
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The 1.9.1 release holds the bug fixes found after releasing 1.9.0 beta.  
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These bugs were primarily replication issues.  There is no difference 
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in functionality between 1.9.0 and 1.9.1 
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Release Notes for 1.9.0:
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------------------------
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This release focuses on simplifying the Metacat installation process by 
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creating a binary (war) installation.  The need to build the application
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on the server has been removed (although the option is still available).
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In order to facilitate this method of installation, a few major modifications
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were made to the code:
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  -- Ant token replacement was removed for all non-build variables in the 
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     application (most of this was already done in 1.8.1).
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  -- The Metacat properties confguration was moved into the application
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     itself.
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  -- Database schema version detection and install/upgrade utilities were 
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     added to the application.
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Also, this release includes several enhancements:
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  -- it supports the new EML 2.1.0 version.  
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  -- Documents are now stored on the local filesystem as well as in the 
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     database in order to preserve document integrity.
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  -- Metacat verifies new schemas when they are added.
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  -- Additional access is propegated with documents during replication.
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High priority bugs were addressed in this release as well.
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The enhancements/bugs addressed are:
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* escaped "less than" in inlinedata causes invalid eml output (Bug 2564)
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* need to set filename for download files (Bug 2566)
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* add ability for search engines to index metacat documents (Bug 2826)
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* EML citation section should include both organizationNames and individualNames (Bug 3059)
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* refactor skins to get organization list from metacat getOrganizations() function (Bug 3114)
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* Update dataknp.sanparks.org packageId attributes to match Metacat Ids (Bug 3258)
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* New documents explicitly set as public access don't show up correctly (Bug 3262)
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* Modify confguration utility in metacat (Bug 3371)
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* Integrate perl token replacement changes (Bug 3372)
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* Create skin specific configuration utility (Bug 3373)
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* Add authentication for configuration utility (Bug 3374)
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* Create a sorted properties utility (Bug 3375)
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* Add DB upgrade/install functionality to java code (Bug 3376)
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* Create ANT install target for developers (Bug 3377)
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* Create LSID server installation (Bug 3380)
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* Create unit test code for 1.9 additions (Bug 3381)
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* create simple turnkey installer for metacat Phase I (Bug 3461)
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* Maps do not display in Firefox version 3 (Bug 3462)
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* Replicate access rules in replication (Bug 3464)
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* Metacat casesensitive="true" option in pathquery expressions is broken (Bug 3472)
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* Add full schema checking when metacat register new schema (Bug 3474)
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* Incorporate EML 2.1.0 access changes in metacat (Bug 3495)
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* getprincipals action returns invalid XML document (Bug 3527)
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* Update knbweb to serve new metacat install (Bug 3545)
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* Replication should write to disk (Bug 3554)
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* Update acknowlegements in metacat readme (Bug 3588)
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* Validate the ldap administrator field. (Bug 3616)
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* Allow for different authentication services in metacat configuration (Bug 3680)
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* Tag utilities module and have metacat check out that tag (Bug 3685)
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Release Notes for 1.8.1:
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------------------------
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This release focuses on bug fixes. In this release, the problem that Metacat 1.8.0 and previous 
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versions use illegitimate EML 2.0.1 schemas is addressed: first, Metacat 1.8.1 comes with
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legitimate EML 2.0.1 schemas; second, existing invalid EML 2.0.1 documents will be 
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automatically fixed while maintaining their package ID during the Metacat 1.8.1 upgrading process. 
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Details please see:
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http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3239
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http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3241
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Note: after upgrading the Metacat to version 1.8.1, some replication issues may be seen, e.g., the 
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EML 2.0.1 documents from Metacat 1.8.0 or ealier verions may be rejected since Metacat 1.8.1 uses
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different EML 2.0.1 schemas (see bug 3239). If this is case, Metacat administrators should notify
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their counterparts to upgrade previous version Metacats to 1.8.1. 
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The fixed bugs include:
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*Character set (charset) problem when filling out form (Bug2797)
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*Charset bug: > "less than" symbol does not display correctly (Bug2517)
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*Metacat performance issue in Sanparks skin (Bug 3174)
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*Metacat using illegitimate versions of EML schema (Bug 3239)
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*Update older invalidated eml201 document in Metacat (Bug 3241)
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*Verify existing token changes to skins (Bug 3176)
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*The edit feature in the NCEAS Data Repoistory does not work (Bug 2644)
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*Expose permission options for registry uploads (Bug 3014)
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*ESA registry doesn't have LTER in login dropdown menu (Bug 2647)
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*Data Catalog Map is slow when selecting (Bug2732)
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*Only one attribute per element returned with pathquery results(Bug 2999)
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*The field "skinconfigs" in the MetacatUtil class is public (Bug 3057)
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*Generalize the reading of skin.configs in DBTransform (Bug3058)
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*The query example in metacatquery.html document need to be changed (Bug3137)
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*Add upload method into Metacat tour (Bug 3139)
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*Query resultset doesn't show component name in kepler skin (Bug 3178)
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*Add fields used in Morpho search to the default indexPaths property (Bug 3259)
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*Private data cannot be downloaded from metadata display page (xsl) (Bug 3263)
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*An error message happen during the metacat start up (Bug 3279)
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*Replication: Timed replication failures occur twice instead of once (Bug 3304)
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*Inline Data does not work correctly without the <pre> tag (Bug 3088)
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*Include FGDC metadata in KNB and NCEAS skin search results (Bug 3146)
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Release Notes for 1.8.0:
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------------------------
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This release focuses on improving query performance.  Both the selection 
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and access control queries were rewritten to execute efficiently.
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To improve search performance, a query caching mechanism was introduced. 
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Cached queries are currently supported only for public users.
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New Features:
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* Data registries now support uploading of data objects along with data 
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  packages (Bug 1982)
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Bug Fixes:
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* Metacat Performace: Rewrite the xml_nodes queries (Bug 2155)
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* Metacat Performace: Rewrite the xml_access part of the query (Bug 2557)
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* Query cache mechanism (Bug 2905)
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* Metacat Performance: updates from Morpho of data packages are taking 
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   longer than five minutes (Bug 2805)
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* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
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* Metacat Performace: Upgrading hardware setup (Bug 2175)
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* Metacat Performace: Add/drop indices on key columns (Bug 2153)
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* Display of metadata documents reorganized, including a new citation format,
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  obvious download options, and a redesigned data table layout (Bugs 2981, 2832)
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* I.E. display fixes on default skin (Bug 2579)
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* Web Address links fixed (Bug 2147)
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* NCEAS skin redesigned to use IFRAME-less layout, match new website.
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* Spatial query:  data packages must be fully contained by the selection 
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  bounding box in order to appear in the search results (Bugs 2972, 2732).
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* FGDC support: upload, delete, update, access control, and download
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  (Bugs 2807, 2925, 2926, 2929, 2030).
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Compatibility Notices:
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* Tomcat 3 and 4 are no longer tested or supported. Users are 
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  highly encouraged to upgrade to Tomcat 5.5
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Release Notes for 1.7.0:
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------------------------
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This release features only a few minor changes to the core Metacat engine. 
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The major focus of this release is the addition of the spatial functionality.
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The geographic coverage of metadata documents can now be cached in a GIS-
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accessible format and published via web mapping services and an online
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interactive map. 
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New Features:
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* Three new open source libraries have been integrated with Metacat:
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  - Geoserver:  A standards-compliant web map server to publish
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                geographic data to the web.
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               (http://docs.codehaus.org/display/GEOS/Home)
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  - GeoTools:   A java-based GIS toolkit to programatically
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                manipulate spatial datasets.
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                (http://geotools.codehaus.org/)
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  - Mapbuilder: A javascript application to provide an interactive
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                web map front-end to Geoserver.
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                (http://docs.codehaus.org/display/MAP/Home)
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* Spatial Caching/Indexing mechanism; documents with geographic
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  coverages will be added to the spatial cache.
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* Spatial Query action in metacat servlet. 
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* Interactive Web map to visualize and query the spatial 
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  distribution of metadata documents.
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* Experimental python, ruby and php client libraries to interface with metacat.
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* Preliminary process in place for web based configuration of metacat.
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Compatibility Notices:
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* Tomcat 3 and 4 are no longer tested or supported. Users are 
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  highly encouraged to upgrade to Tomcat 5.5
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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
442
  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:
465
 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 
467
    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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------------------------
473

    
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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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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 
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     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.
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Fixes in 1.3.0:
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  1) Couldn't finish delta T replication for large set of documents.
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  2) Couldn't create access control during delta T replication.
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  3) Eorr will be written to a seperated log file if some documents
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     were failed in replication.
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  4) Decrease the time to create access rules during insert or update 
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     a package.
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Documentation
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-------------
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See the docs directory for detailed documentation and installation
518
instructions.
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Details of the Metacat architecture can be found on the website for
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the Knowledge Network for Biocomplexity (KNB):
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  http://knb.ecoinformatics.org/software/metacat/
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Contributions to this work are welcome.  Please see the above web site
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for details on how to contribute.
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Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
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-----------------------------------------------------------------------------
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If you discover a bug please report it, either by email (above) or by using
531
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
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for the next release.
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Legalese
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--------
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This software is copyrighted by The Regents of the University of California
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and the National Center for Ecological Analysis and Synthesis
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and licensed under the GNU GPL; see the 'LICENSE' file for
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details.
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This material is based upon work supported by the
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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 
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expressed in this material are those of the author(s) and do not necessarily 
546
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. 
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Mellon Foundation.
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This product includes software developed by the Apache Software
552
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
553
for details.
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The source code, object code, and documentation in the com.oreilly.servlet
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package is copyright and owned by Jason Hunter. See the cos-license.html file
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for details of the license.  Licensor retains title to and ownership of the
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Software and all enhancements, modifications, and updates to the Software.
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This software includes the JDBC driver for PostgreSQL.  See the 
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postgresql-license.txt file for details.