Project

General

Profile

metacat / README @ 3955

1
#
2
#  '$RCSfile$'
3
#   '$Author: tao $'
4
# '$Revision: 3955 $'
5
#     '$Date: 2008-06-09 16:43:53 -0700 (Mon, 09 Jun 2008) $'
6
#
7

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

    
11
Version: 1.8.1 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
              John Harris (harris@nceas.ucsb.edu)
25
              Callie Bowdish (bowdish@ecoinformatics.org)
26
              Will Tyburczy (tyburczy@ecoinformatics.org)
27
              Matthew Perry (perry@nceas.ucsb.edu)
28
              Chad Burt (underbluewaters@gmail.com)
29
              Ben Leinfelder (leinfelder@nceas.ucsb.edu)
30
              Chris Barteau (barteau@nceas.ucsb.edu)
31
              Shaun Walbridge (walbridge@nceas.ucsb.edu)
32
              Michael Daigle (daigle@nceas.ucsb.edu) 
33

    
34
Patch contributors:
35
              Andrea Chadden (chadden@nceas.ucsb.edu)
36
              Chris Jones (cjones@msi.ucsb.edu)
37
              Johnoel Ancheta (johnoel@hawaii.edu)
38
              Owen Jones (owen.jones@imperial.ac.uk)
39

    
40
Metacat is a flexible database storage system for XML formatted
41
documents and associated binary files. Metacat models the structure of the
42
XML document, therefore allowing storage of XML documents with arbitrary
43
schemas. Metacat supports several databases on the back-end, including Oracle,
44
PostgreSQL and SQL Server (limited).  The server supports XML document
45
storage, retrieval, query, validation, and transformation (using the XSLT
46
stylesheet language).  In addition, there is a mechanism for replicating the
47
database to other metacat instances for backup and load balancing purposes.
48
Metacat currently uses an LDAP database for authenticating users, but was
49
written to accomodate other authentication services as well.
50

    
51
Installation
52
------------
53
See the file "docs/user/metacatinstall.html" for detailed instructions.
54

    
55
Release Notes for 1.8.1:
56
------------------------
57
This release focuses on bug fixes. In this release, the problem that Metacat 1.8.0 and previous 
58
versions use illegitimate EML 2.0.1 schemas is addressed: first, Metacat 1.8.1 comes with
59
legitimate EML 2.0.1 schemas; second, existing invalid EML 2.0.1 documents will be 
60
automatically fixed while maintaining their package ID during the Metacat 1.8.1 upgrading process. 
61
Details please see:
62
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3239
63
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3241
64

    
65
Note: after upgrading the Metacat to version 1.8.1, some replication issues may be seen, e.g., the 
66
EML 2.0.1 documents from Metacat 1.8.0 or ealier verions may be rejected since Metacat 1.8.1 uses
67
different EML 2.0.1 schemas (see bug 3239). If this is case, Metacat administrators should notify
68
their counterparts to upgrade previous version Metacats to 1.8.1. 
69

    
70
The fixed bugs include:
71

    
72
*Character set (charset) problem when filling out form (Bug2797)
73
*Charset bug: > "less than" symbol does not display correctly (Bug2517)
74
*Metacat performance issue in Sanparks skin (Bug 3174)
75
*Metacat using illegitimate versions of EML schema (Bug 3239)
76
*Update older invalidated eml201 document in Metacat (Bug 3241)
77
*Verify existing token changes to skins (Bug 3176)
78
*The edit feature in the NCEAS Data Repoistory does not work (Bug 2644)
79
*Expose permission options for registry uploads (Bug 3014)
80
*ESA registry doesn't have LTER in login dropdown menu (Bug 2647)
81
*Data Catalog Map is slow when selecting (Bug2732)
82
*Only one attribute per element returned with pathquery results(Bug 2999)
83
*The field "skinconfigs" in the MetacatUtil class is public (Bug 3057)
84
*Generalize the reading of skin.configs in DBTransform (Bug3058)
85
*The query example in metacatquery.html document need to be changed (Bug3137)
86
*Add upload method into Metacat tour (Bug 3139)
87
*Query resultset doesn't show component name in kepler skin (Bug 3178)
88
*Add fields used in Morpho search to the default indexPaths property (Bug 3259)
89
*Private data cannot be downloaded from metadata display page (xsl) (Bug 3263)
90
*An error message happen during the metacat start up (Bug 3279)
91
*Replication: Timed replication failures occur twice instead of once (Bug 3304)
92
*Inline Data does not work correctly without the <pre> tag (Bug 3088)
93
*Include FGDC metadata in KNB and NCEAS skin search results (Bug 3146)
94

    
95
Release Notes for 1.8.0:
96
------------------------
97
This release focuses on improving query performance.  Both the selection 
98
and access control queries were rewritten to execute efficiently.
99
To improve search performance, a query caching mechanism was introduced. 
100
Cached queries are currently supported only for public users.
101

    
102
New Features:
103
* Data registries now support uploading of data objects along with data 
104
  packages (Bug 1982)
105
  
106
Bug Fixes:
107
* Metacat Performace: Rewrite the xml_nodes queries (Bug 2155)
108
* Metacat Performace: Rewrite the xml_access part of the query (Bug 2557)
109
* Query cache mechanism (Bug 2905)
110
* Metacat Performance: updates from Morpho of data packages are taking 
111
   longer than five minutes (Bug 2805)
112
* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
113
* Metacat Performace: Upgrading hardware setup (Bug 2175)
114
* Metacat Performace: Add/drop indices on key columns (Bug 2153)
115
* Display of metadata documents reorganized, including a new citation format,
116
  obvious download options, and a redesigned data table layout (Bugs 2981, 2832)
117
* I.E. display fixes on default skin (Bug 2579)
118
* Web Address links fixed (Bug 2147)
119
* NCEAS skin redesigned to use IFRAME-less layout, match new website.
120
* Spatial query:  data packages must be fully contained by the selection 
121
  bounding box in order to appear in the search results (Bugs 2972, 2732).
122
* FGDC support: upload, delete, update, access control, and download
123
  (Bugs 2807, 2925, 2926, 2929, 2030).
124
Compatibility Notices:
125
* Tomcat 3 and 4 are no longer tested or supported. Users are 
126
  highly encouraged to upgrade to Tomcat 5.5
127

    
128
Release Notes for 1.7.0:
129
------------------------
130
This release features only a few minor changes to the core Metacat engine. 
131
The major focus of this release is the addition of the spatial functionality.
132
The geographic coverage of metadata documents can now be cached in a GIS-
133
accessible format and published via web mapping services and an online
134
interactive map. 
135

    
136
New Features:
137
* Three new open source libraries have been integrated with Metacat:
138
  - Geoserver:  A standards-compliant web map server to publish
139
                geographic data to the web.
140
               (http://docs.codehaus.org/display/GEOS/Home)
141
  - GeoTools:   A java-based GIS toolkit to programatically
142
                manipulate spatial datasets.
143
                (http://geotools.codehaus.org/)
144
  - Mapbuilder: A javascript application to provide an interactive
145
                web map front-end to Geoserver.
146
                (http://docs.codehaus.org/display/MAP/Home)
147
* Spatial Caching/Indexing mechanism; documents with geographic
148
  coverages will be added to the spatial cache.
149
* Spatial Query action in metacat servlet. 
150
* Interactive Web map to visualize and query the spatial 
151
  distribution of metadata documents.
152
* Experimental python, ruby and php client libraries to interface with metacat.
153
* Preliminary process in place for web based configuration of metacat.
154

    
155
Compatibility Notices:
156
* Tomcat 3 and 4 are no longer tested or supported. Users are 
157
  highly encouraged to upgrade to Tomcat 5.5
158

    
159
Bug Fixes:
160
* Metacat administrators are able to modify and delete documents 
161
  created by other users.
162
* Fixed problems with indexing XML attributes, see bug 2469
163

    
164

    
165
Release Notes for 1.6.0:
166
------------------------
167

    
168
This release comes with more performance improvements, initial support for 
169
LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for 
170
Metacat administrators and bug fixes. Below is the list of bug fixes and
171
performance improvements.
172

    
173
Bug Fixes: 
174
* Improved the indexing algorithm. Earlier indexing failed for some documents 
175
  randomly and used to take a lot of time to complete for others. The 
176
  code for indexing was changed to take care of both these problems.
177
* Earlier, xmlns prefix was used to determine the namespace of the document. 
178
  Now schemaLocation is used instead xmlns prefix to determine the namespace 
179
  of the document as that is a better indicator of document type. 
180
* INSTR was used in some SQL statements and it is not supported by Postgres. 
181
  So SQL statements were modified so that INSTR is not used.
182
* Replication was changed to include replication of deleted documents also.
183
* Fixed bug in squery which didnt allow use of not-contains 
184

    
185
New Features:
186
* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
187
* Added support for LSID. This includes modifying the stylesheets to 
188
  display the LSIDs, modifying the build to include a new target 
189
  'install-ldap'.
190
* Added following access control levels to Metacat:
191
    1. Administrators - users who can do the following:
192
       a. Run replication
193
       b. Delete any document
194
       c. Modify any document
195
       d. run indexing for any document
196
       e. check the logs
197
    2. allowedUsers - User who are allowed to submit
198
    3. deniedUsers - Users not allowed to submit
199
* Added a new skin for Ecological Society of America. 
200
* Created an Advanced search servlet which can be used from the web. 
201
* Various connections have been modified to be secure. e.g. connection between 
202
ldaps is made secure now, replication is done over secure channels.  
203

    
204
Performance:
205
* Reduced size of xml_nodes by creating a new table for holding nodes from 
206
  deleted documents and old revisions of the documents. 
207
* Provided a new variable in metacat.properties where more frequently searched 
208
  for paths can be specified. Seperate indexes are created for these paths 
209
  - so that search is faster.
210
* Included log4j for logging and debuging to prevent wasting of time in printing log statements. 
211

    
212
Release Notes for 1.5.0:
213
------------------------
214

    
215
This release comes with performace improvement, user interface enhancements,
216
and bug fixes. Below is the list of bug fixes and performance improvements. 
217

    
218
Bug Fixes:
219
* Modify property values of harvester registration servlets to match the
220
  servlet-mapping URL values in web.xml. The old values used the servlet
221
  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
222
  Windows. The new values use the servlet-mapping URL values. This should
223
  work in both Tomcat 4 and Tomcat 5. (Bug 162)
224
* Re-implement logic to prune old log entries from the HARVEST_LOG and
225
  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
226
  violations in the database because it tried to delete parent records from
227
  HARVEST_LOG prior to deleting child records from
228
  HARVEST_DETAIL_LOG. (Bug 162)
229
* In data registry, minor bugs fixed like the error page shows the link back
230
  to the form when error page was generated because of a document read
231
  request from search results page,  the successful delete button leading
232
  to a blank screen and the old ACL overwritten by the registry.
233
  (Bugs 1307, 1310, 1322, 1344, 1551)
234
* Changed the code to support insertion of following characters: ', `,
235
  charcters in the Numeric Character Reference format (&#xyz;) and
236
  characters like µ. Characters like µ will be converted to and stored in
237
  Numeric Character Reference format(&#xyz;). They will also be returned
238
  in Numeric Character Reference and it is upto the client to convert them
239
  and display them accordingly in the application. Partial fix provided by
240
  Johnoel Ancheta. (Bug 1538,1711)
241
* Spatial search failed on Oracle because of invalid entries made by
242
  some documents in the nodedata column of xml_nodes for paths involving
243
  'eastBoundingCoordinate', 'westBoundingCoordinate',
244
  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
245
  nodedatanumerical was added to xml_nodes table such that all the numerical
246
  nodedata is stored in this column and this column is now used for spatial
247
  search. (Bug 1703, 1718)
248
* In the default skin, clicking on the keywords on the home page did not
249
  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
250
* Metacat generated a success message even when a document which didnt
251
  exsist was requested for deletion. This has been fixed. (Bug 1850)
252
* "packagetype" in xml-relation table was entered as eml200 namespace when
253
  an eml201 document was inserted. This is fixed now so that "packagetype"
254
  in xml-relation table points to eml201 namespace. (Bug 1979)
255
* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
256
  earlier. Fixed such that it points to the locally installed metacat url. 
257
  (Bug 1986)
258
* Changes to the Query subsystem fix bugs that prevented attributes from 
259
  being expressed solely in the xpath query statement and the returnfield 
260
  values. For instance, a query URL may now include search strings like 
261
  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
262
  Previously, the attribute had to be appended to an element: 
263
  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
264
  QuerySpecification.java, and QueryTerm.java (Bug 2052)
265
* Search query failed in case of Oracle if number of documents in the result
266
  were more than 1000. This has been fixed. (Bug 2000)
267
* Removed any occurence of enum which is now a keyword in Java 1.5
268

    
269

    
270
Enhancements:
271
* Major improvements done in user interface for the data registeries and
272
  various other skins. Improvements done based on suggestions from Mark
273
  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
274
  the default skin and ldap templates. (Bug 1948)
275
* Coded added such that administrator can delete documents irrespective of
276
  who the document belongs to.
277
* Performance impovement done in searching of datasets. A part of the search
278
  time was taken up because of generation of resultset after the search had be
279
  done. So this was the sequence of events in earlier metacat
280
  1) Search for the given text
281
  2) A list of docids generated
282
  3) For each of the docids
283
     3a) Use xml_index and xml_nodes table to generate the string descibing
284
         the document including the returnfields requested in the search
285
  4) Add all the strings from step 3a to send back the resultant
286
     document. Here a decent amount of time was being taken by step 3a. 
287
  The algorithm is now modified by addition of two tables xml_queryresult and
288
  xml_returnfields and a user defined parameter xml_returnfield_count. The
289
  new algorithm works as follows:
290
  1) Search for the given text
291
  2) A list of docids is generated
292
  3) For the given set of return fields generate a unique string and check
293
     if that string exists in xml_returnfields
294
     3a) If string does not exist in xml_returnfield, then enter a new
295
         record usage_count as 1 and returnfield_string as the unique string
296
         generated above.
297
     3b) Else if the string exists, increment usage_count
298
  4) Given the docids from step 2 and the id of the returnfield record from
299
     step 3, query for any docids that already exist in xml_queryresult.
300
     For the docids that do exist, get the queryresult_string.
301
  5) For rest of the docids from step2 which were not found in step 4, do
302
     the following for each of the documents:
303
     5a) Use xml_index and xml_nodes table to generate the string descibing
304
         the document including the returnfields requested in the search
305
     5b) If usage_count of the record from step is more than
306
         xml_returnfield_count set in metacat.properties, then store the
307
         string in xml_queryresult as a record which has the returnfield_id
308
         representing the set of returnfields, docid representing the
309
         document and the string as queryresult_string.
310
  6) Add all the strings from step 4 and step 5a to send back the resultant
311
     document
312
  So the results from step 3a in previous algorithm are effectively cached
313
  and hence same computation is not done again and again for each search.
314
  When a document is deleted, all the entries for that document in
315
  xml_queryresult table are also deleted. When a document is updated, all
316
  the entries for that document in xml_queryresult table are deleted. This
317
  works fine because those entries will be generated and cached again the
318
  next time the document is part of a search is requested.
319
* Performance impovement done for % search.
320
* Following new functions added to metacat client API: a method to set access
321
  on an xml document and a method to get newest version for a given document.
322
* Implement a new HarvesterServlet for running Harvester as a servlet. This
323
  eliminates the need to run Harvester in a terminal window. By default, the
324
  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
325
  documentation will be modified to instruct Harvester administrators to
326
  uncomment the HarvesterServlet entry.
327
* Minor enhancement to support multiple email addresses for harvester
328
  administrator and site contact. Each address is separated by a comma or
329
  semicolon.
330
* Increase number of rows in Harvest List Editor from 300 to 1200.
331
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
332
  value when it is set to 0 or a negative number. This allows Harvester to
333
  run indefinitely without shutting down after reaching a maximum number of
334
  harvests. The previous default value of 30 would cause Harvester to
335
  terminate after 30 harvests.
336

    
337
Details of all changes can be found in the bug database here:
338
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
339

    
340

    
341
Release Notes for 1.4.0:
342
------------------------
343

    
344
This is a major release, and is the first to introduce many new features to
345
Metacat.  Some of the major new features in this version of Metacat include:
346

    
347
* Added a new 'Harvester' that allows documents to be periodically pulled
348
  from distributed sources into metacat, useful for interfacing with other
349
  system types. See the Metacat Tour for details.
350
* Added new 'skins' capability to allow the GUI for the metacat web interface
351
  to be more easily customized to fit into site needs.  The skin is based on
352
  a flexible mix of XSLT, CSS, and Javascript.
353
* Added a web-based metadata entry form for submitting limited EML documents
354
  as part of a data registry.  The GUI for the registry is customizable and 
355
  is integrated with the 'skins' system for the main metacat interface.  The
356
  registry subsystem is written in Perl, and can simultaneously be used to 
357
  present multiple 'registry' interfaces.
358
* A new 'client API' has been developed and implemented in Java and in Perl 
359
  so that metacat functions can be accessed from any program in those
360
  languages.  The client API supports the major metacat servlet actions,
361
  including login(), logout(), query(), insert(), update(), delete(), and 
362
  upload(). See the Metacat Tour for details.
363
* Added a new 'getlog' action that produces a usage history for all major
364
  events.  So now an XML report can be generated for document reads, inserts,
365
  deletes, etc.  See the new section in the Metacat Tour.
366
* Added a new 'buildindex' action that can rebuild the index entries for any
367
  document in the database.
368
* The configuration file for metacat (metacat.properties) has been moved out
369
  of the jar file and into the WEB-INF directory, allowing far easier changes
370
  to the configuration parameters.
371
* Results in default web interface are sorted by title in the XSLT 
372
  (configurable)
373
* Many bugs were fixed.
374

    
375
Details of all changes can be found in the bug database here:
376
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
377

    
378
Release Notes for 1.3.1:
379
------------------------
380

    
381
This is a simple interim bug fix. No major functionality changes. Bugs fixed 
382
include:
383
 1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in 
384
    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3 
385
    and Java 1.4.
386
 2) Distribution package size was reduced.
387

    
388

    
389
Release Notes for 1.3.0
390
------------------------
391

    
392
In 1.3.0 release, the structure of the xml_access table was changed and a new
393
table, xml_accesssubtree was added. If you try to update a previously 
394
installed Metacat, you should run a script file to updated the table structure 
395
before installation.
396
For Oracle user: At the SQLPLUS prompt type the following -
397
@src/reviseformetacat13.sql
398
For Postgresql user: At install directory prompt type the following -
399
psql exp < src/reviseformetacat13_postgres.sql
400
(where 'exp' is the database name).
401

    
402
After installation, user should run "ant schemasql" command to register EML2
403
schema in xml_catalog table.
404

    
405
If you are a new Metacat user, this step is unneeded.
406

    
407
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise, 
408
         it will cause potential replication issues.
409
      2) Delete the xercesImpl.jar and xmlParserAPIs.jar files 
410
         which are in $CATALINA_HOME/common/endorsed. They are old version and
411
         don't support XML schema validation.
412

    
413
New Features in 1.3.0
414
  1) Partialy support EML2 document. User can store, query, read and write
415
     EML2 documents. However, Metacat only support access control in resource
416
     level. The subtree level access control will be ignored.
417
  2) Support other xml document base on namespace/schema.
418
  3) Support query for attribute value
419
  4) Assign MIME type to data file base on metadata when user try to read it.
420
  5) Owner can assign access rules to a document which does not have access 
421
     document to apply it.
422
  6) Support exporting single file, not only whole package
423
  7) Resupport Microsoft SQL Server.
424

    
425
Fixes in 1.3.0:
426
  1) Couldn't finish delta T replication for large set of documents.
427
  2) Couldn't create access control during delta T replication.
428
  3) Eorr will be written to a seperated log file if some documents
429
     were failed in replication.
430
  4) Decrease the time to create access rules during insert or update 
431
     a package.
432
     
433
Documentation
434
-------------
435
See the docs directory for detailed documentation and installation
436
instructions.
437

    
438
Details of the Metacat architecture can be found on the website for
439
the Knowledge Network for Biocomplexity (KNB):
440

    
441
  http://knb.ecoinformatics.org/software/metacat/
442

    
443
Contributions to this work are welcome.  Please see the above web site
444
for details on how to contribute.
445

    
446
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
447
-----------------------------------------------------------------------------
448
If you discover a bug please report it, either by email (above) or by using
449
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
450
list of currently unimplemented features in Bugzilla that we are working on
451
for the next release.
452

    
453
Legalese
454
--------
455
This software is copyrighted by The Regents of the University of California
456
and the National Center for Ecological Analysis and Synthesis
457
and licensed under the GNU GPL; see the 'LICENSE' file for
458
details.
459

    
460
This material is based upon work supported by the
461
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
462
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations 
463
expressed in this material are those of the author(s) and do not necessarily 
464
reflect the views of the National Science Foundation (NSF).
465

    
466
This software is partially supported by a grant from the Andrew W. 
467
Mellon Foundation.
468

    
469
This product includes software developed by the Apache Software
470
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
471
for details.
472

    
473
The source code, object code, and documentation in the com.oreilly.servlet
474
package is copyright and owned by Jason Hunter. See the cos-license.html file
475
for details of the license.  Licensor retains title to and ownership of the
476
Software and all enhancements, modifications, and updates to the Software.
477

    
478
This software includes the JDBC driver for PostgreSQL.  See the 
479
postgresql-license.txt file for details.