Project

General

Profile

metacat / README @ 8448

1
#
2
#  '$RCSfile$'
3
#   '$Author: leinfelder $'
4
# '$Revision: 8448 $'
5
#     '$Date: 2013-12-19 10:19:01 -0800 (Thu, 19 Dec 2013) $'
6
#
7

    
8
Metacat: XML Metadata and Data Management System
9
------------------------------------------------                      
10

    
11
Version: 2.3.1 Release
12

    
13
Send feedback and bugs to: metacat-dev@ecoinformatics.org
14
                           http://bugzilla.ecoinformatics.org
15

    
16
Contributors: Matt Jones (jones@nceas.ucsb.edu)
17
              Chad Berkley (berkley@nceas.ucsb.edu)
18
              Jing Tao (tao@nceas.ucsb.edu)
19
              Jivka Bojilova (bojilova@nceas.ucsb.edu)
20
              Dan Higgins (higgins@nceas.ucsb.edu)
21
              Saurabh Garg (sgarg@nceas.ucsb.edu)
22
              Duane Costa (dcosta@lternet.edu)
23
              Veronique Connolly (connolly@nceas.ucsb.edu)
24
              Chris Jones (cjones@msi.ucsb.edu)
25
              John Harris (harris@nceas.ucsb.edu)
26
              Callie Bowdish (bowdish@ecoinformatics.org)
27
              Will Tyburczy (tyburczy@ecoinformatics.org)
28
              Matthew Perry (perry@nceas.ucsb.edu)
29
              Chad Burt (underbluewaters@gmail.com)
30
              Ben Leinfelder (leinfelder@nceas.ucsb.edu)
31
              Chris Barteau (barteau@nceas.ucsb.edu)
32
              Shaun Walbridge (walbridge@nceas.ucsb.edu)
33
              Michael Daigle (daigle@nceas.ucsb.edu) 
34
              Lauren Walker (walker@nceas.ucsb.edu) 
35

    
36
Patch contributors:
37
              Andrea Chadden (chadden@nceas.ucsb.edu)
38
              Johnoel Ancheta (johnoel@hawaii.edu)
39
              Owen Jones (owen.jones@imperial.ac.uk)
40

    
41
Metacat is a flexible database storage system for XML formatted
42
documents and associated binary files. Metacat models the structure of the
43
XML document, therefore allowing storage of XML documents with arbitrary
44
schemas. Metacat supports several databases on the back-end, including Oracle,
45
PostgreSQL and SQL Server (limited).  The server supports XML document
46
storage, retrieval, query, validation, and transformation (using the XSLT
47
stylesheet language).  In addition, there is a mechanism for replicating the
48
database to other metacat instances for backup and load balancing purposes.
49
Metacat currently uses an LDAP database for authenticating users, but was
50
written to accomodate other authentication services as well.
51

    
52
Installation
53
------------
54
See the file "docs/install.html" for detailed instructions
55
for your OS.
56

    
57
Release Notes for 2.3.1:
58
------------------------
59
This is a minor patch release to fix an issue that arises when
60
Metacat is operating as a DataONE Coordinating Node.
61
* See: https://projects.ecoinformatics.org/ecoinfo/issues/6315
62
* Updated MetacatUI with support for spatial query criteria
63
* Updated account/identity management script
64

    
65
Release Notes for 2.3.0:
66
------------------------
67
This release adds solr indexing features to metacat-index 
68
for querying and sorting by authors and taxonomic coverage.
69
Also includes:
70
* Control over the log level from the SOLR libraries using Metacat's
71
log4j file.
72
* access_log DB indexes for better log reporting performance 
73
via the DataONE API
74
* Provide 'reindexall' action instead of 'reindex' without a 'pid' parameter.
75

    
76

    
77
Release Notes for 2.2.1:
78
------------------------
79
This is a critical patch release of Metacat that includes addresses
80
a bug in file stream handling. It is recommended for all Metacat deployments.
81

    
82
Release Notes for 2.2.0:
83
------------------------
84
This is a major release of Metacat that includes a new customizable UI and 
85
improved LDAP account management features
86

    
87
Release Notes for 2.1.1:
88
------------------------
89
This is a minor patch release of Metacat that addresses
90
a bug in DOI publishing.
91

    
92
Release Notes for 2.1.0:
93
------------------------
94
This is a major release of Metacat that includes a SOLR-based search feature
95
* Optional SOLR search index
96
* Client certificate delegation (using a service provider like CILogon)
97

    
98
Release Notes for 2.0.8:
99
------------------------
100
This is a patch release for Metacat
101
* Enforce DataONE prohibition on whitespace in identifiers
102
* Use unique filenames for Registry data uploads
103

    
104
Release Notes for 2.0.7:
105
------------------------
106
This is a patch release for Metacat replication
107
* Replication SQL performance enhancement
108
* Comply with DataONE schema for SystemMetadata.submitter
109

    
110
Release Notes for 2.0.6:
111
------------------------
112
This patch release focuses on Metacat support for DataONE-enabled Morpho clients
113
* MN.generateIdentifier() support for UUID and DOI
114
* DOI registration support using EZID service
115
* Pathquery support for specifying multiple document owners
116

    
117

    
118
Release Notes for 2.0.5:
119
------------------------
120
This patch release focuses on Metacat support for Oracle
121
*SystemMetadata table names have been shortened to comply with Oracle limits.
122
*SANParks/SAEON spatial zip file download fixed
123
*Pathquery performance fix
124
*Hazelcast 2.x upgrade
125
*Correct handling for deleted and archived objects for both Metacat and DataONE APIs
126

    
127
Release Notes for 2.0.4:
128
------------------------
129
This patch release focuses on Metacat-Metacat replication.
130
*Allows Metacat to stream replication update information between servers to avoid connection timeout issues
131
*Allows Metacat replication when source host does not provide SystemMetadata (DataONE)
132
*Fixes an access control issue that could allow search results to include protected documents
133

    
134
Release Notes for 2.0.3:
135
------------------------
136
This is another critical patch release of Metacat 2.0.
137
*Addresses a bug that prevented Metacat replication from completing (timeout error)
138
*Uses more efficient SystemMetadata synchronization using shared Hazelcast map
139

    
140
Release Notes for 2.0.2:
141
------------------------
142
This is a critical patch release of Metacat 2.0.
143
*Addresses a bug that prevented updates to DataONE identified datapackages (e.g., using DOIs)
144
*Addresses a bug that prevented the use of the Metacat API 'getaccesscontrol' action
145
*Updates the Foresite ORE library to correctly serialize resource map documents
146

    
147
Release Notes for 2.0.1:
148
------------------------
149
This is a minor patch release of Metacat 2.0. Please see the previous release notes for complete information.
150
*Addresses an identifier issue during ORE generation for DataONE services
151
*Increases compatibility with older EML content and the Xalan XSLT processor
152
*Removes XSLT 2.0 support (Saxon)
153

    
154
Release Notes for 2.0.0:
155
------------------------
156
This major release includes support for DataONE.
157
*The DataONE v1.0.0 Member Node service APIs are now the preferred method for communicating with Metacat
158
*The existing EcoGrid and Metacat Servlet APIs are deprecated but still available.
159
*EML-embedded access control rules using permOrder="denyFirst" are no longer supported (https://redmine.dataone.org/issues/2614) 
160
*Replication now utilizes client certificates to establish SSL connections between replication source and target servers
161
*Access control rules now apply to objects on a per-revision basis rather than per-docid
162
*Bugs fixed include:
163
-SANParks skin/TPC (5561, 5530, 5533, 5542, 5543, 5544, 5551, 5563, 5566, 5567, 5569, 5353)
164
-Registry (5114, 5244)
165
-Replication (4907, 5537, 5536, 5534, 5520, 5519, 3296)
166
-Spatial cache regeneration can be skipped during reconfiguration/redeployment/upgrade (3811)
167
-Pathquery support for temporal search criteria (2084)
168
-Character encoding of XML now respected (internationalization) (2495, 4083, 3815)
169

    
170

    
171
Release Notes for 1.9.5:
172
------------------------
173
This release fixes those bugs:
174
*Metacat could not download the included schemas in an external schema file during inserting.
175
*Workflow scheduler could not work since the metadata standard of kepler kar file was changed. 
176
*Earthgrid could not transform the Earthgrid query with concept "/" to the Metacat path query correctly.
177
*Document access rules are now preserved when documents are archived during the 'delete' action.
178

    
179
Release Notes for 1.9.4:
180
------------------------
181
This release fixes bugs in the FGDC data package upload and download interface utilized
182
by the SANParks and SAEON skins.
183

    
184
Release Notes for 1.9.3:
185
------------------------
186
This release fixes a harvester bug that prevented the EML harvester from processing
187
harvest lists.
188
The Kepler skin has been updated to support KarXML 2.1.
189
Ecogrid query services now support multiple namespace searches.
190

    
191
Release Notes for 1.9.2:
192
------------------------
193
This release primarily holds the addition of the Threshold of Potential
194
Concern workflow functionality (TPC).  The following issues were addressed:
195

    
196
* Create a properties file for use by JUnit Tests (Bug 2994)
197
* security issue with skins (Bug 3368)
198
* reorganize classes into a more functional specific structure (Bug 3510)
199
* Add admin names as dropdown in configuration login (Bug 3729)
200
* KNB metacat replication error log file is empty (Bug 3885)
201
* Create TPC Report web browse/search pages (Bug 4165)
202
* Create archive extraction functionality (Bug 4166)
203
* Create Workflow Scheduler (Bug 4167)
204
* metacat didn't update xml_path_index table while a document was updated (Bug 4367)
205
* Enforce permissions for tpc workflow viewing and scheduling (Bug 4420)
206
* Fix cross platform TPC GUI issues (Bug 4556)
207
* TPC Sanparks page content lenth issue (Bug 4557)
208
* Create validate and isAuthorized unit tests (Bug 4558)
209
* Cannot insert replication server via gui (Bug 4594)
210
* Timed Replication takes many hours and drives the load up on KNB (Bug 4616)
211
* [ESA] Update fails when document rev number is missing (Bug 4627)
212
* fails to catch some insert and update failures (Bug 4637)
213
* must support java 1.6 (Bug 4641)
214
* Convert build to pull eml from svn instead of cvs (Bug 4644)
215
* handleGetRevisionAndDocTypeAction should search both xml_documents and xml_revisions table (Bug 4645)
216
* Metacat couldn't update a document from client, which previous versions only stay in xml_revisions table (Bug 4649)
217
* metacat runs out of memory (Bug 4658)
218
* ESA skin links are hard coded to data.esa.org (Bug 4698)
219
* Update release 1.9.2 release notes (Bug 4707)
220
* Handle writing a text node > 4000 characters to the db. (Bug 4708)
221
* Metacat should run against Tomcat 6 (Bug 4716)
222

    
223
Release Notes for 1.9.1:
224
------------------------
225
The 1.9.1 release holds the bug fixes found after releasing 1.9.0 beta.  
226
These bugs were primarily replication issues.  There is no difference 
227
in functionality between 1.9.0 and 1.9.1 
228

    
229
Release Notes for 1.9.0:
230
------------------------
231
This release focuses on simplifying the Metacat installation process by 
232
creating a binary (war) installation.  The need to build the application
233
on the server has been removed (although the option is still available).
234
In order to facilitate this method of installation, a few major modifications
235
were made to the code:
236

    
237
  -- Ant token replacement was removed for all non-build variables in the 
238
     application (most of this was already done in 1.8.1).
239

    
240
  -- The Metacat properties confguration was moved into the application
241
     itself.
242

    
243
  -- Database schema version detection and install/upgrade utilities were 
244
     added to the application.
245

    
246
Also, this release includes several enhancements:
247
  -- it supports the new EML 2.1.0 version.  
248

    
249
  -- Documents are now stored on the local filesystem as well as in the 
250
     database in order to preserve document integrity.
251
     
252
  -- Metacat verifies new schemas when they are added.
253

    
254
  -- Additional access is propegated with documents during replication.
255

    
256
High priority bugs were addressed in this release as well.
257

    
258
The enhancements/bugs addressed are:
259

    
260
* escaped "less than" in inlinedata causes invalid eml output (Bug 2564)
261
* need to set filename for download files (Bug 2566)
262
* add ability for search engines to index metacat documents (Bug 2826)
263
* EML citation section should include both organizationNames and individualNames (Bug 3059)
264
* refactor skins to get organization list from metacat getOrganizations() function (Bug 3114)
265
* Update dataknp.sanparks.org packageId attributes to match Metacat Ids (Bug 3258)
266
* New documents explicitly set as public access don't show up correctly (Bug 3262)
267
* Modify confguration utility in metacat (Bug 3371)
268
* Integrate perl token replacement changes (Bug 3372)
269
* Create skin specific configuration utility (Bug 3373)
270
* Add authentication for configuration utility (Bug 3374)
271
* Create a sorted properties utility (Bug 3375)
272
* Add DB upgrade/install functionality to java code (Bug 3376)
273
* Create ANT install target for developers (Bug 3377)
274
* Create LSID server installation (Bug 3380)
275
* Create unit test code for 1.9 additions (Bug 3381)
276
* create simple turnkey installer for metacat Phase I (Bug 3461)
277
* Maps do not display in Firefox version 3 (Bug 3462)
278
* Replicate access rules in replication (Bug 3464)
279
* Metacat casesensitive="true" option in pathquery expressions is broken (Bug 3472)
280
* Add full schema checking when metacat register new schema (Bug 3474)
281
* Incorporate EML 2.1.0 access changes in metacat (Bug 3495)
282
* getprincipals action returns invalid XML document (Bug 3527)
283
* Update knbweb to serve new metacat install (Bug 3545)
284
* Replication should write to disk (Bug 3554)
285
* Update acknowlegements in metacat readme (Bug 3588)
286
* Validate the ldap administrator field. (Bug 3616)
287
* Allow for different authentication services in metacat configuration (Bug 3680)
288
* Tag utilities module and have metacat check out that tag (Bug 3685)
289

    
290
Release Notes for 1.8.1:
291
------------------------
292
This release focuses on bug fixes. In this release, the problem that Metacat 1.8.0 and previous 
293
versions use illegitimate EML 2.0.1 schemas is addressed: first, Metacat 1.8.1 comes with
294
legitimate EML 2.0.1 schemas; second, existing invalid EML 2.0.1 documents will be 
295
automatically fixed while maintaining their package ID during the Metacat 1.8.1 upgrading process. 
296
Details please see:
297
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3239
298
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3241
299

    
300
Note: after upgrading the Metacat to version 1.8.1, some replication issues may be seen, e.g., the 
301
EML 2.0.1 documents from Metacat 1.8.0 or ealier verions may be rejected since Metacat 1.8.1 uses
302
different EML 2.0.1 schemas (see bug 3239). If this is case, Metacat administrators should notify
303
their counterparts to upgrade previous version Metacats to 1.8.1. 
304

    
305
The fixed bugs include:
306

    
307
*Character set (charset) problem when filling out form (Bug2797)
308
*Charset bug: > "less than" symbol does not display correctly (Bug2517)
309
*Metacat performance issue in Sanparks skin (Bug 3174)
310
*Metacat using illegitimate versions of EML schema (Bug 3239)
311
*Update older invalidated eml201 document in Metacat (Bug 3241)
312
*Verify existing token changes to skins (Bug 3176)
313
*The edit feature in the NCEAS Data Repoistory does not work (Bug 2644)
314
*Expose permission options for registry uploads (Bug 3014)
315
*ESA registry doesn't have LTER in login dropdown menu (Bug 2647)
316
*Data Catalog Map is slow when selecting (Bug2732)
317
*Only one attribute per element returned with pathquery results(Bug 2999)
318
*The field "skinconfigs" in the MetacatUtil class is public (Bug 3057)
319
*Generalize the reading of skin.configs in DBTransform (Bug3058)
320
*The query example in metacatquery.html document need to be changed (Bug3137)
321
*Add upload method into Metacat tour (Bug 3139)
322
*Query resultset doesn't show component name in kepler skin (Bug 3178)
323
*Add fields used in Morpho search to the default indexPaths property (Bug 3259)
324
*Private data cannot be downloaded from metadata display page (xsl) (Bug 3263)
325
*An error message happen during the metacat start up (Bug 3279)
326
*Replication: Timed replication failures occur twice instead of once (Bug 3304)
327
*Inline Data does not work correctly without the <pre> tag (Bug 3088)
328
*Include FGDC metadata in KNB and NCEAS skin search results (Bug 3146)
329

    
330
Release Notes for 1.8.0:
331
------------------------
332
This release focuses on improving query performance.  Both the selection 
333
and access control queries were rewritten to execute efficiently.
334
To improve search performance, a query caching mechanism was introduced. 
335
Cached queries are currently supported only for public users.
336

    
337
New Features:
338
* Data registries now support uploading of data objects along with data 
339
  packages (Bug 1982)
340
  
341
Bug Fixes:
342
* Metacat Performace: Rewrite the xml_nodes queries (Bug 2155)
343
* Metacat Performace: Rewrite the xml_access part of the query (Bug 2557)
344
* Query cache mechanism (Bug 2905)
345
* Metacat Performance: updates from Morpho of data packages are taking 
346
   longer than five minutes (Bug 2805)
347
* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
348
* Metacat Performace: Upgrading hardware setup (Bug 2175)
349
* Metacat Performace: Add/drop indices on key columns (Bug 2153)
350
* Display of metadata documents reorganized, including a new citation format,
351
  obvious download options, and a redesigned data table layout (Bugs 2981, 2832)
352
* I.E. display fixes on default skin (Bug 2579)
353
* Web Address links fixed (Bug 2147)
354
* NCEAS skin redesigned to use IFRAME-less layout, match new website.
355
* Spatial query:  data packages must be fully contained by the selection 
356
  bounding box in order to appear in the search results (Bugs 2972, 2732).
357
* FGDC support: upload, delete, update, access control, and download
358
  (Bugs 2807, 2925, 2926, 2929, 2030).
359
Compatibility Notices:
360
* Tomcat 3 and 4 are no longer tested or supported. Users are 
361
  highly encouraged to upgrade to Tomcat 5.5
362

    
363
Release Notes for 1.7.0:
364
------------------------
365
This release features only a few minor changes to the core Metacat engine. 
366
The major focus of this release is the addition of the spatial functionality.
367
The geographic coverage of metadata documents can now be cached in a GIS-
368
accessible format and published via web mapping services and an online
369
interactive map. 
370

    
371
New Features:
372
* Three new open source libraries have been integrated with Metacat:
373
  - Geoserver:  A standards-compliant web map server to publish
374
                geographic data to the web.
375
               (http://docs.codehaus.org/display/GEOS/Home)
376
  - GeoTools:   A java-based GIS toolkit to programatically
377
                manipulate spatial datasets.
378
                (http://geotools.codehaus.org/)
379
  - Mapbuilder: A javascript application to provide an interactive
380
                web map front-end to Geoserver.
381
                (http://docs.codehaus.org/display/MAP/Home)
382
* Spatial Caching/Indexing mechanism; documents with geographic
383
  coverages will be added to the spatial cache.
384
* Spatial Query action in metacat servlet. 
385
* Interactive Web map to visualize and query the spatial 
386
  distribution of metadata documents.
387
* Experimental python, ruby and php client libraries to interface with metacat.
388
* Preliminary process in place for web based configuration of metacat.
389

    
390
Compatibility Notices:
391
* Tomcat 3 and 4 are no longer tested or supported. Users are 
392
  highly encouraged to upgrade to Tomcat 5.5
393

    
394
Bug Fixes:
395
* Metacat administrators are able to modify and delete documents 
396
  created by other users.
397
* Fixed problems with indexing XML attributes, see bug 2469
398

    
399

    
400
Release Notes for 1.6.0:
401
------------------------
402

    
403
This release comes with more performance improvements, initial support for 
404
LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for 
405
Metacat administrators and bug fixes. Below is the list of bug fixes and
406
performance improvements.
407

    
408
Bug Fixes: 
409
* Improved the indexing algorithm. Earlier indexing failed for some documents 
410
  randomly and used to take a lot of time to complete for others. The 
411
  code for indexing was changed to take care of both these problems.
412
* Earlier, xmlns prefix was used to determine the namespace of the document. 
413
  Now schemaLocation is used instead xmlns prefix to determine the namespace 
414
  of the document as that is a better indicator of document type. 
415
* INSTR was used in some SQL statements and it is not supported by Postgres. 
416
  So SQL statements were modified so that INSTR is not used.
417
* Replication was changed to include replication of deleted documents also.
418
* Fixed bug in squery which didnt allow use of not-contains 
419

    
420
New Features:
421
* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
422
* Added support for LSID. This includes modifying the stylesheets to 
423
  display the LSIDs, modifying the build to include a new target 
424
  'install-ldap'.
425
* Added following access control levels to Metacat:
426
    1. Administrators - users who can do the following:
427
       a. Run replication
428
       b. Delete any document
429
       c. Modify any document
430
       d. run indexing for any document
431
       e. check the logs
432
    2. allowedUsers - User who are allowed to submit
433
    3. deniedUsers - Users not allowed to submit
434
* Added a new skin for Ecological Society of America. 
435
* Created an Advanced search servlet which can be used from the web. 
436
* Various connections have been modified to be secure. e.g. connection between 
437
ldaps is made secure now, replication is done over secure channels.  
438

    
439
Performance:
440
* Reduced size of xml_nodes by creating a new table for holding nodes from 
441
  deleted documents and old revisions of the documents. 
442
* Provided a new variable in metacat.properties where more frequently searched 
443
  for paths can be specified. Seperate indexes are created for these paths 
444
  - so that search is faster.
445
* Included log4j for logging and debuging to prevent wasting of time in printing log statements. 
446

    
447
Release Notes for 1.5.0:
448
------------------------
449

    
450
This release comes with performace improvement, user interface enhancements,
451
and bug fixes. Below is the list of bug fixes and performance improvements. 
452

    
453
Bug Fixes:
454
* Modify property values of harvester registration servlets to match the
455
  servlet-mapping URL values in web.xml. The old values used the servlet
456
  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
457
  Windows. The new values use the servlet-mapping URL values. This should
458
  work in both Tomcat 4 and Tomcat 5. (Bug 162)
459
* Re-implement logic to prune old log entries from the HARVEST_LOG and
460
  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
461
  violations in the database because it tried to delete parent records from
462
  HARVEST_LOG prior to deleting child records from
463
  HARVEST_DETAIL_LOG. (Bug 162)
464
* In data registry, minor bugs fixed like the error page shows the link back
465
  to the form when error page was generated because of a document read
466
  request from search results page,  the successful delete button leading
467
  to a blank screen and the old ACL overwritten by the registry.
468
  (Bugs 1307, 1310, 1322, 1344, 1551)
469
* Changed the code to support insertion of following characters: ', `,
470
  charcters in the Numeric Character Reference format (&#xyz;) and
471
  characters like µ. Characters like µ will be converted to and stored in
472
  Numeric Character Reference format(&#xyz;). They will also be returned
473
  in Numeric Character Reference and it is upto the client to convert them
474
  and display them accordingly in the application. Partial fix provided by
475
  Johnoel Ancheta. (Bug 1538,1711)
476
* Spatial search failed on Oracle because of invalid entries made by
477
  some documents in the nodedata column of xml_nodes for paths involving
478
  'eastBoundingCoordinate', 'westBoundingCoordinate',
479
  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
480
  nodedatanumerical was added to xml_nodes table such that all the numerical
481
  nodedata is stored in this column and this column is now used for spatial
482
  search. (Bug 1703, 1718)
483
* In the default skin, clicking on the keywords on the home page did not
484
  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
485
* Metacat generated a success message even when a document which didnt
486
  exsist was requested for deletion. This has been fixed. (Bug 1850)
487
* "packagetype" in xml-relation table was entered as eml200 namespace when
488
  an eml201 document was inserted. This is fixed now so that "packagetype"
489
  in xml-relation table points to eml201 namespace. (Bug 1979)
490
* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
491
  earlier. Fixed such that it points to the locally installed metacat url. 
492
  (Bug 1986)
493
* Changes to the Query subsystem fix bugs that prevented attributes from 
494
  being expressed solely in the xpath query statement and the returnfield 
495
  values. For instance, a query URL may now include search strings like 
496
  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
497
  Previously, the attribute had to be appended to an element: 
498
  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
499
  QuerySpecification.java, and QueryTerm.java (Bug 2052)
500
* Search query failed in case of Oracle if number of documents in the result
501
  were more than 1000. This has been fixed. (Bug 2000)
502
* Removed any occurence of enum which is now a keyword in Java 1.5
503

    
504

    
505
Enhancements:
506
* Major improvements done in user interface for the data registeries and
507
  various other skins. Improvements done based on suggestions from Mark
508
  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
509
  the default skin and ldap templates. (Bug 1948)
510
* Coded added such that administrator can delete documents irrespective of
511
  who the document belongs to.
512
* Performance impovement done in searching of datasets. A part of the search
513
  time was taken up because of generation of resultset after the search had be
514
  done. So this was the sequence of events in earlier metacat
515
  1) Search for the given text
516
  2) A list of docids generated
517
  3) For each of the docids
518
     3a) Use xml_index and xml_nodes table to generate the string descibing
519
         the document including the returnfields requested in the search
520
  4) Add all the strings from step 3a to send back the resultant
521
     document. Here a decent amount of time was being taken by step 3a. 
522
  The algorithm is now modified by addition of two tables xml_queryresult and
523
  xml_returnfields and a user defined parameter xml_returnfield_count. The
524
  new algorithm works as follows:
525
  1) Search for the given text
526
  2) A list of docids is generated
527
  3) For the given set of return fields generate a unique string and check
528
     if that string exists in xml_returnfields
529
     3a) If string does not exist in xml_returnfield, then enter a new
530
         record usage_count as 1 and returnfield_string as the unique string
531
         generated above.
532
     3b) Else if the string exists, increment usage_count
533
  4) Given the docids from step 2 and the id of the returnfield record from
534
     step 3, query for any docids that already exist in xml_queryresult.
535
     For the docids that do exist, get the queryresult_string.
536
  5) For rest of the docids from step2 which were not found in step 4, do
537
     the following for each of the documents:
538
     5a) Use xml_index and xml_nodes table to generate the string descibing
539
         the document including the returnfields requested in the search
540
     5b) If usage_count of the record from step is more than
541
         xml_returnfield_count set in metacat.properties, then store the
542
         string in xml_queryresult as a record which has the returnfield_id
543
         representing the set of returnfields, docid representing the
544
         document and the string as queryresult_string.
545
  6) Add all the strings from step 4 and step 5a to send back the resultant
546
     document
547
  So the results from step 3a in previous algorithm are effectively cached
548
  and hence same computation is not done again and again for each search.
549
  When a document is deleted, all the entries for that document in
550
  xml_queryresult table are also deleted. When a document is updated, all
551
  the entries for that document in xml_queryresult table are deleted. This
552
  works fine because those entries will be generated and cached again the
553
  next time the document is part of a search is requested.
554
* Performance impovement done for % search.
555
* Following new functions added to metacat client API: a method to set access
556
  on an xml document and a method to get newest version for a given document.
557
* Implement a new HarvesterServlet for running Harvester as a servlet. This
558
  eliminates the need to run Harvester in a terminal window. By default, the
559
  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
560
  documentation will be modified to instruct Harvester administrators to
561
  uncomment the HarvesterServlet entry.
562
* Minor enhancement to support multiple email addresses for harvester
563
  administrator and site contact. Each address is separated by a comma or
564
  semicolon.
565
* Increase number of rows in Harvest List Editor from 300 to 1200.
566
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
567
  value when it is set to 0 or a negative number. This allows Harvester to
568
  run indefinitely without shutting down after reaching a maximum number of
569
  harvests. The previous default value of 30 would cause Harvester to
570
  terminate after 30 harvests.
571

    
572
Details of all changes can be found in the bug database here:
573
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
574

    
575

    
576
Release Notes for 1.4.0:
577
------------------------
578

    
579
This is a major release, and is the first to introduce many new features to
580
Metacat.  Some of the major new features in this version of Metacat include:
581

    
582
* Added a new 'Harvester' that allows documents to be periodically pulled
583
  from distributed sources into metacat, useful for interfacing with other
584
  system types. See the Metacat Tour for details.
585
* Added new 'skins' capability to allow the GUI for the metacat web interface
586
  to be more easily customized to fit into site needs.  The skin is based on
587
  a flexible mix of XSLT, CSS, and Javascript.
588
* Added a web-based metadata entry form for submitting limited EML documents
589
  as part of a data registry.  The GUI for the registry is customizable and 
590
  is integrated with the 'skins' system for the main metacat interface.  The
591
  registry subsystem is written in Perl, and can simultaneously be used to 
592
  present multiple 'registry' interfaces.
593
* A new 'client API' has been developed and implemented in Java and in Perl 
594
  so that metacat functions can be accessed from any program in those
595
  languages.  The client API supports the major metacat servlet actions,
596
  including login(), logout(), query(), insert(), update(), delete(), and 
597
  upload(). See the Metacat Tour for details.
598
* Added a new 'getlog' action that produces a usage history for all major
599
  events.  So now an XML report can be generated for document reads, inserts,
600
  deletes, etc.  See the new section in the Metacat Tour.
601
* Added a new 'buildindex' action that can rebuild the index entries for any
602
  document in the database.
603
* The configuration file for metacat (metacat.properties) has been moved out
604
  of the jar file and into the WEB-INF directory, allowing far easier changes
605
  to the configuration parameters.
606
* Results in default web interface are sorted by title in the XSLT 
607
  (configurable)
608
* Many bugs were fixed.
609

    
610
Details of all changes can be found in the bug database here:
611
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
612

    
613
Release Notes for 1.3.1:
614
------------------------
615

    
616
This is a simple interim bug fix. No major functionality changes. Bugs fixed 
617
include:
618
 1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in 
619
    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3 
620
    and Java 1.4.
621
 2) Distribution package size was reduced.
622

    
623

    
624
Release Notes for 1.3.0
625
------------------------
626

    
627
In 1.3.0 release, the structure of the xml_access table was changed and a new
628
table, xml_accesssubtree was added. If you try to update a previously 
629
installed Metacat, you should run a script file to updated the table structure 
630
before installation.
631
For Oracle user: At the SQLPLUS prompt type the following -
632
@src/reviseformetacat13.sql
633
For Postgresql user: At install directory prompt type the following -
634
psql exp < src/reviseformetacat13_postgres.sql
635
(where 'exp' is the database name).
636

    
637
After installation, user should run "ant schemasql" command to register EML2
638
schema in xml_catalog table.
639

    
640
If you are a new Metacat user, this step is unneeded.
641

    
642
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise, 
643
         it will cause potential replication issues.
644
      2) Delete the xercesImpl.jar and xmlParserAPIs.jar files 
645
         which are in $CATALINA_HOME/common/endorsed. They are old version and
646
         don't support XML schema validation.
647

    
648
New Features in 1.3.0
649
  1) Partialy support EML2 document. User can store, query, read and write
650
     EML2 documents. However, Metacat only support access control in resource
651
     level. The subtree level access control will be ignored.
652
  2) Support other xml document base on namespace/schema.
653
  3) Support query for attribute value
654
  4) Assign MIME type to data file base on metadata when user try to read it.
655
  5) Owner can assign access rules to a document which does not have access 
656
     document to apply it.
657
  6) Support exporting single file, not only whole package
658
  7) Resupport Microsoft SQL Server.
659

    
660
Fixes in 1.3.0:
661
  1) Couldn't finish delta T replication for large set of documents.
662
  2) Couldn't create access control during delta T replication.
663
  3) Eorr will be written to a seperated log file if some documents
664
     were failed in replication.
665
  4) Decrease the time to create access rules during insert or update 
666
     a package.
667
     
668
Documentation
669
-------------
670
See the docs directory for detailed documentation and installation
671
instructions.
672

    
673
Details of the Metacat architecture can be found on the website for
674
the Knowledge Network for Biocomplexity (KNB):
675

    
676
  http://knb.ecoinformatics.org/software/metacat/
677

    
678
Contributions to this work are welcome.  Please see the above web site
679
for details on how to contribute.
680

    
681
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
682
-----------------------------------------------------------------------------
683
If you discover a bug please report it, either by email (above) or by using
684
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
685
list of currently unimplemented features in Bugzilla that we are working on
686
for the next release.
687

    
688
Legalese
689
--------
690
This software is copyrighted by The Regents of the University of California
691
and the National Center for Ecological Analysis and Synthesis
692
and licensed under the GNU GPL; see the 'LICENSE' file for
693
details.
694

    
695
This material is based upon work supported by the
696
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
697
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations 
698
expressed in this material are those of the author(s) and do not necessarily 
699
reflect the views of the National Science Foundation (NSF).
700

    
701
This software is partially supported by a grant from the Andrew W. 
702
Mellon Foundation.
703

    
704
This product includes software developed by the Apache Software
705
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
706
for details.
707

    
708
The source code, object code, and documentation in the com.oreilly.servlet
709
package is copyright and owned by Jason Hunter. See the cos-license.html file
710
for details of the license.  Licensor retains title to and ownership of the
711
Software and all enhancements, modifications, and updates to the Software.
712

    
713
This software includes the JDBC driver for PostgreSQL.  See the 
714
postgresql-license.txt file for details.