Project

General

Profile

1 981 tao
#
2 666 jones
#  '$RCSfile$'
3
#   '$Author$'
4
# '$Revision$'
5
#     '$Date$'
6
#
7
8 2479 jones
Metacat: XML Metadata and Data Management System
9
------------------------------------------------
10 666 jones
11 3621 tao
Version: 1.8.0 Release
12 666 jones
13 1295 jones
Send feedback and bugs to: metacat-dev@ecoinformatics.org
14
                           http://bugzilla.ecoinformatics.org
15 696 jones
16 666 jones
Contributors: Matt Jones (jones@nceas.ucsb.edu)
17
              Chad Berkley (berkley@nceas.ucsb.edu)
18 981 tao
              Jing Tao (tao@nceas.ucsb.edu)
19 666 jones
              Jivka Bojilova (bojilova@nceas.ucsb.edu)
20
              Dan Higgins (higgins@nceas.ucsb.edu)
21 2313 jones
              Saurabh Garg (sgarg@nceas.ucsb.edu)
22
              Duane Costa (dcosta@lternet.edu)
23 2480 jones
              Veronique Connolly (connolly@nceas.ucsb.edu)
24 2905 harris
              John Harris (harris@nceas.ucsb.edu)
25
              Callie Bowdish (bowdish@ecoinformatics.org)
26
              Will Tyburczy (tyburczy@ecoinformatics.org)
27 3020 sgarg
              Matthew Perry (perry@nceas.ucsb.edu)
28 3130 perry
              Chad Burt (underbluewaters@gmail.com)
29 3612 walbridge
              Ben Leinfelder (leinfelder@nceas.ucsb.edu)
30
              Chris Barteau (barteau@nceas.ucsb.edu)
31
              Shaun Walbridge (walbridge@nceas.ucsb.edu)
32 2480 jones
33
Patch contributors:
34
              Andrea Chadden (chadden@nceas.ucsb.edu)
35 2479 jones
              Chris Jones (cjones@msi.ucsb.edu)
36 2480 jones
              Johnoel Ancheta (johnoel@hawaii.edu)
37
              Owen Jones (owen.jones@imperial.ac.uk)
38 1311 berkley
39 982 berkley
Metacat is a flexible database storage system for XML formatted
40 2313 jones
documents and associated binary files. Metacat models the structure of the
41
XML document, therefore allowing storage of XML documents with arbitrary
42
schemas. Metacat supports several databases on the back-end, including Oracle,
43
PostgreSQL and SQL Server (limited).  The server supports XML document
44 2441 jones
storage, retrieval, query, validation, and transformation (using the XSLT
45 2313 jones
stylesheet language).  In addition, there is a mechanism for replicating the
46
database to other metacat instances for backup and load balancing purposes.
47
Metacat currently uses an LDAP database for authenticating users, but was
48
written to accomodate other authentication services as well.
49 666 jones
50 2321 jones
Installation
51
------------
52
See the file "docs/user/metacatinstall.html" for detailed instructions.
53
54 3621 tao
Release Notes for 1.8.0:
55 3376 tao
------------------------
56 3612 walbridge
This release focuses on improving query performance.  Both the selection
57
and access control queries were rewritten to execute efficiently.
58
To improve search performance, a query caching mechanism was introduced.
59
Cached queries are currently supported only for public users.
60 3376 tao
61 3612 walbridge
New Features:
62
* Data registries now support uploading of data objects along with data
63
  packages (Bug 1982)
64
65 3376 tao
Bug Fixes:
66
* Metacat Performace: Rewrite the xml_nodes queries (Bug 2155)
67
* Metacat Performace: Rewrite the xml_access part of the query (Bug 2557)
68
* Query cache mechanism (Bug 2905)
69
* Metacat Performance: updates from Morpho of data packages are taking
70
   longer than five minutes (Bug 2805)
71 3613 leinfelder
* Metacat Performance: Optimize Postgres and Tomcat (Bug 2157)
72 3376 tao
* Metacat Performace: Upgrading hardware setup (Bug 2175)
73
* Metacat Performace: Add/drop indices on key columns (Bug 2153)
74 3612 walbridge
* Display of metadata documents reorganized, including a new citation format,
75 3614 bowdish
  obvious download options, and a redesigned data table layout (Bugs 2981, 2832)
76
* I.E. display fixes on default skin (Bug 2579)
77
* Web Address links fixed (Bug 2147)
78 3612 walbridge
* NCEAS skin redesigned to use IFRAME-less layout, match new website.
79 3613 leinfelder
* Spatial query:  data packages must be fully contained by the selection
80 3614 bowdish
  bounding box in order to appear in the search results (Bugs 2972, 2732).
81 3628 barteau
* FGDC support: upload, delete, update, access control, and download
82
  (Bugs 2807, 2925, 2926, 2929, 2030).
83 3376 tao
Compatibility Notices:
84
* Tomcat 3 and 4 are no longer tested or supported. Users are
85
  highly encouraged to upgrade to Tomcat 5.5
86
87 3109 perry
Release Notes for 1.7.0:
88
------------------------
89
This release features only a few minor changes to the core Metacat engine.
90
The major focus of this release is the addition of the spatial functionality.
91
The geographic coverage of metadata documents can now be cached in a GIS-
92
accessible format and published via web mapping services and an online
93
interactive map.
94 3020 sgarg
95 3109 perry
New Features:
96
* Three new open source libraries have been integrated with Metacat:
97
  - Geoserver:  A standards-compliant web map server to publish
98
                geographic data to the web.
99 3614 bowdish
               (http://docs.codehaus.org/display/GEOS/Home)
100 3109 perry
  - GeoTools:   A java-based GIS toolkit to programatically
101
                manipulate spatial datasets.
102
                (http://geotools.codehaus.org/)
103
  - Mapbuilder: A javascript application to provide an interactive
104
                web map front-end to Geoserver.
105
                (http://docs.codehaus.org/display/MAP/Home)
106
* Spatial Caching/Indexing mechanism; documents with geographic
107
  coverages will be added to the spatial cache.
108
* Spatial Query action in metacat servlet.
109
* Interactive Web map to visualize and query the spatial
110
  distribution of metadata documents.
111 3135 perry
* Experimental python, ruby and php client libraries to interface with metacat.
112 3109 perry
* Preliminary process in place for web based configuration of metacat.
113
114
Compatibility Notices:
115
* Tomcat 3 and 4 are no longer tested or supported. Users are
116
  highly encouraged to upgrade to Tomcat 5.5
117
118
Bug Fixes:
119
* Metacat administrators are able to modify and delete documents
120
  created by other users.
121 3153 jones
* Fixed problems with indexing XML attributes, see bug 2469
122 3109 perry
123
124 3020 sgarg
Release Notes for 1.6.0:
125
------------------------
126
127
This release comes with more performance improvements, initial support for
128
LSIDs (Life Sciences Identifiers) and FGDC standard, more controls for
129
Metacat administrators and bug fixes. Below is the list of bug fixes and
130
performance improvements.
131
132
Bug Fixes:
133
* Improved the indexing algorithm. Earlier indexing failed for some documents
134
  randomly and used to take a lot of time to complete for others. The
135
  code for indexing was changed to take care of both these problems.
136
* Earlier, xmlns prefix was used to determine the namespace of the document.
137
  Now schemaLocation is used instead xmlns prefix to determine the namespace
138
  of the document as that is a better indicator of document type.
139
* INSTR was used in some SQL statements and it is not supported by Postgres.
140
  So SQL statements were modified so that INSTR is not used.
141 3025 sgarg
* Replication was changed to include replication of deleted documents also.
142
* Fixed bug in squery which didnt allow use of not-contains
143 3020 sgarg
144
New Features:
145
* Added FGDC schema and XSLT so that Metacat can handle FGDC standard
146
* Added support for LSID. This includes modifying the stylesheets to
147
  display the LSIDs, modifying the build to include a new target
148
  'install-ldap'.
149
* Added following access control levels to Metacat:
150
    1. Administrators - users who can do the following:
151
       a. Run replication
152
       b. Delete any document
153
       c. Modify any document
154
       d. run indexing for any document
155
       e. check the logs
156
    2. allowedUsers - User who are allowed to submit
157
    3. deniedUsers - Users not allowed to submit
158
* Added a new skin for Ecological Society of America.
159 3025 sgarg
* Created an Advanced search servlet which can be used from the web.
160
* Various connections have been modified to be secure. e.g. connection between
161
ldaps is made secure now, replication is done over secure channels.
162 3020 sgarg
163
Performance:
164
* Reduced size of xml_nodes by creating a new table for holding nodes from
165
  deleted documents and old revisions of the documents.
166
* Provided a new variable in metacat.properties where more frequently searched
167
  for paths can be specified. Seperate indexes are created for these paths
168
  - so that search is faster.
169 3025 sgarg
* Included log4j for logging and debuging to prevent wasting of time in printing log statements.
170 3020 sgarg
171 2475 sgarg
Release Notes for 1.5.0:
172
------------------------
173
174 2479 jones
This release comes with performace improvement, user interface enhancements,
175 2475 sgarg
and bug fixes. Below is the list of bug fixes and performance improvements.
176
177
Bug Fixes:
178
* Modify property values of harvester registration servlets to match the
179
  servlet-mapping URL values in web.xml. The old values used the servlet
180
  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
181
  Windows. The new values use the servlet-mapping URL values. This should
182
  work in both Tomcat 4 and Tomcat 5. (Bug 162)
183
* Re-implement logic to prune old log entries from the HARVEST_LOG and
184
  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
185
  violations in the database because it tried to delete parent records from
186
  HARVEST_LOG prior to deleting child records from
187
  HARVEST_DETAIL_LOG. (Bug 162)
188
* In data registry, minor bugs fixed like the error page shows the link back
189
  to the form when error page was generated because of a document read
190
  request from search results page,  the successful delete button leading
191
  to a blank screen and the old ACL overwritten by the registry.
192
  (Bugs 1307, 1310, 1322, 1344, 1551)
193
* Changed the code to support insertion of following characters: ', `,
194
  charcters in the Numeric Character Reference format (&#xyz;) and
195
  characters like µ. Characters like µ will be converted to and stored in
196
  Numeric Character Reference format(&#xyz;). They will also be returned
197
  in Numeric Character Reference and it is upto the client to convert them
198
  and display them accordingly in the application. Partial fix provided by
199
  Johnoel Ancheta. (Bug 1538,1711)
200
* Spatial search failed on Oracle because of invalid entries made by
201
  some documents in the nodedata column of xml_nodes for paths involving
202
  'eastBoundingCoordinate', 'westBoundingCoordinate',
203
  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
204
  nodedatanumerical was added to xml_nodes table such that all the numerical
205
  nodedata is stored in this column and this column is now used for spatial
206
  search. (Bug 1703, 1718)
207
* In the default skin, clicking on the keywords on the home page did not
208
  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
209
* Metacat generated a success message even when a document which didnt
210
  exsist was requested for deletion. This has been fixed. (Bug 1850)
211
* "packagetype" in xml-relation table was entered as eml200 namespace when
212
  an eml201 document was inserted. This is fixed now so that "packagetype"
213
  in xml-relation table points to eml201 namespace. (Bug 1979)
214
* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
215
  earlier. Fixed such that it points to the locally installed metacat url.
216
  (Bug 1986)
217
* Changes to the Query subsystem fix bugs that prevented attributes from
218
  being expressed solely in the xpath query statement and the returnfield
219
  values. For instance, a query URL may now include search strings like
220
  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
221
  Previously, the attribute had to be appended to an element:
222
  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java,
223
  QuerySpecification.java, and QueryTerm.java (Bug 2052)
224
* Search query failed in case of Oracle if number of documents in the result
225
  were more than 1000. This has been fixed. (Bug 2000)
226
* Removed any occurence of enum which is now a keyword in Java 1.5
227
228
229
Enhancements:
230
* Major improvements done in user interface for the data registeries and
231
  various other skins. Improvements done based on suggestions from Mark
232
  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
233
  the default skin and ldap templates. (Bug 1948)
234
* Coded added such that administrator can delete documents irrespective of
235
  who the document belongs to.
236
* Performance impovement done in searching of datasets. A part of the search
237
  time was taken up because of generation of resultset after the search had be
238
  done. So this was the sequence of events in earlier metacat
239
  1) Search for the given text
240
  2) A list of docids generated
241
  3) For each of the docids
242
     3a) Use xml_index and xml_nodes table to generate the string descibing
243
         the document including the returnfields requested in the search
244 2479 jones
  4) Add all the strings from step 3a to send back the resultant
245
     document. Here a decent amount of time was being taken by step 3a.
246
  The algorithm is now modified by addition of two tables xml_queryresult and
247
  xml_returnfields and a user defined parameter xml_returnfield_count. The
248
  new algorithm works as follows:
249 2475 sgarg
  1) Search for the given text
250 2479 jones
  2) A list of docids is generated
251 2475 sgarg
  3) For the given set of return fields generate a unique string and check
252
     if that string exists in xml_returnfields
253
     3a) If string does not exist in xml_returnfield, then enter a new
254
         record usage_count as 1 and returnfield_string as the unique string
255
         generated above.
256
     3b) Else if the string exists, increment usage_count
257
  4) Given the docids from step 2 and the id of the returnfield record from
258
     step 3, query for any docids that already exist in xml_queryresult.
259
     For the docids that do exist, get the queryresult_string.
260
  5) For rest of the docids from step2 which were not found in step 4, do
261
     the following for each of the documents:
262
     5a) Use xml_index and xml_nodes table to generate the string descibing
263
         the document including the returnfields requested in the search
264
     5b) If usage_count of the record from step is more than
265
         xml_returnfield_count set in metacat.properties, then store the
266
         string in xml_queryresult as a record which has the returnfield_id
267
         representing the set of returnfields, docid representing the
268
         document and the string as queryresult_string.
269
  6) Add all the strings from step 4 and step 5a to send back the resultant
270
     document
271
  So the results from step 3a in previous algorithm are effectively cached
272
  and hence same computation is not done again and again for each search.
273
  When a document is deleted, all the entries for that document in
274
  xml_queryresult table are also deleted. When a document is updated, all
275
  the entries for that document in xml_queryresult table are deleted. This
276
  works fine because those entries will be generated and cached again the
277
  next time the document is part of a search is requested.
278
* Performance impovement done for % search.
279
* Following new functions added to metacat client API: a method to set access
280
  on an xml document and a method to get newest version for a given document.
281
* Implement a new HarvesterServlet for running Harvester as a servlet. This
282
  eliminates the need to run Harvester in a terminal window. By default, the
283
  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
284
  documentation will be modified to instruct Harvester administrators to
285
  uncomment the HarvesterServlet entry.
286
* Minor enhancement to support multiple email addresses for harvester
287
  administrator and site contact. Each address is separated by a comma or
288
  semicolon.
289
* Increase number of rows in Harvest List Editor from 300 to 1200.
290
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
291
  value when it is set to 0 or a negative number. This allows Harvester to
292
  run indefinitely without shutting down after reaching a maximum number of
293
  harvests. The previous default value of 30 would cause Harvester to
294
  terminate after 30 harvests.
295
296
Details of all changes can be found in the bug database here:
297
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
298
299
300 2313 jones
Release Notes for 1.4.0:
301
------------------------
302
303
This is a major release, and is the first to introduce many new features to
304
Metacat.  Some of the major new features in this version of Metacat include:
305
306
* Added a new 'Harvester' that allows documents to be periodically pulled
307
  from distributed sources into metacat, useful for interfacing with other
308
  system types. See the Metacat Tour for details.
309
* Added new 'skins' capability to allow the GUI for the metacat web interface
310
  to be more easily customized to fit into site needs.  The skin is based on
311
  a flexible mix of XSLT, CSS, and Javascript.
312 2321 jones
* Added a web-based metadata entry form for submitting limited EML documents
313 2313 jones
  as part of a data registry.  The GUI for the registry is customizable and
314
  is integrated with the 'skins' system for the main metacat interface.  The
315
  registry subsystem is written in Perl, and can simultaneously be used to
316
  present multiple 'registry' interfaces.
317
* A new 'client API' has been developed and implemented in Java and in Perl
318
  so that metacat functions can be accessed from any program in those
319
  languages.  The client API supports the major metacat servlet actions,
320
  including login(), logout(), query(), insert(), update(), delete(), and
321
  upload(). See the Metacat Tour for details.
322
* Added a new 'getlog' action that produces a usage history for all major
323
  events.  So now an XML report can be generated for document reads, inserts,
324
  deletes, etc.  See the new section in the Metacat Tour.
325
* Added a new 'buildindex' action that can rebuild the index entries for any
326
  document in the database.
327
* The configuration file for metacat (metacat.properties) has been moved out
328
  of the jar file and into the WEB-INF directory, allowing far easier changes
329
  to the configuration parameters.
330 2321 jones
* Results in default web interface are sorted by title in the XSLT
331
  (configurable)
332
* Many bugs were fixed.
333 2313 jones
334
Details of all changes can be found in the bug database here:
335
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
336
337 1775 tao
Release Notes for 1.3.1:
338 2313 jones
------------------------
339 1308 tao
340 1775 tao
This is a simple interim bug fix. No major functionality changes. Bugs fixed
341
include:
342 1776 tao
 1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in
343
    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3
344
    and Java 1.4.
345 1775 tao
 2) Distribution package size was reduced.
346
347
348
Release Notes for 1.3.0
349 2313 jones
------------------------
350 1775 tao
351
In 1.3.0 release, the structure of the xml_access table was changed and a new
352 1628 tao
table, xml_accesssubtree was added. If you try to update a previously
353
installed Metacat, you should run a script file to updated the table structure
354
before installation.
355
For Oracle user: At the SQLPLUS prompt type the following -
356
@src/reviseformetacat13.sql
357
For Postgresql user: At install directory prompt type the following -
358
psql exp < src/reviseformetacat13_postgres.sql
359
(where 'exp' is the database name).
360 1334 tao
361 1628 tao
After installation, user should run "ant schemasql" command to register EML2
362
schema in xml_catalog table.
363
364
If you are a new Metacat user, this step is unneeded.
365
366 1769 tao
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise,
367
         it will cause potential replication issues.
368
      2) Delete the xercesImpl.jar and xmlParserAPIs.jar files
369
         which are in $CATALINA_HOME/common/endorsed. They are old version and
370
         don't support XML schema validation.
371
372 1628 tao
New Features in 1.3.0
373
  1) Partialy support EML2 document. User can store, query, read and write
374
     EML2 documents. However, Metacat only support access control in resource
375
     level. The subtree level access control will be ignored.
376
  2) Support other xml document base on namespace/schema.
377
  3) Support query for attribute value
378
  4) Assign MIME type to data file base on metadata when user try to read it.
379
  5) Owner can assign access rules to a document which does not have access
380
     document to apply it.
381
  6) Support exporting single file, not only whole package
382 1769 tao
  7) Resupport Microsoft SQL Server.
383 1628 tao
384
Fixes in 1.3.0:
385
  1) Couldn't finish delta T replication for large set of documents.
386
  2) Couldn't create access control during delta T replication.
387
  3) Eorr will be written to a seperated log file if some documents
388
     were failed in replication.
389
  4) Decrease the time to create access rules during insert or update
390
     a package.
391
392 861 jones
Documentation
393
-------------
394 1311 berkley
See the docs directory for detailed documentation and installation
395 666 jones
instructions.
396
397 1311 berkley
Details of the Metacat architecture can be found on the website for
398 666 jones
the Knowledge Network for Biocomplexity (KNB):
399
400 805 jones
  http://knb.ecoinformatics.org/software/metacat/
401 666 jones
402
Contributions to this work are welcome.  Please see the above web site
403
for details on how to contribute.
404
405 848 jones
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
406
-----------------------------------------------------------------------------
407 2313 jones
If you discover a bug please report it, either by email (above) or by using
408
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
409
list of currently unimplemented features in Bugzilla that we are working on
410
for the next release.
411 805 jones
412
Legalese
413
--------
414 666 jones
This software is copyrighted by The Regents of the University of California
415
and the National Center for Ecological Analysis and Synthesis
416
and licensed under the GNU GPL; see the 'LICENSE' file for
417
details.
418
419 1311 berkley
This material is based upon work supported by the
420 2313 jones
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
421 2975 jones
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations
422
expressed in this material are those of the author(s) and do not necessarily
423
reflect the views of the National Science Foundation (NSF).
424 1307 jones
425 2505 sgarg
This software is partially supported by a grant from the Andrew W.
426
Mellon Foundation.
427
428 1311 berkley
This product includes software developed by the Apache Software
429 1307 jones
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
430
for details.
431
432 1311 berkley
The source code, object code, and documentation in the com.oreilly.servlet
433 1307 jones
package is copyright and owned by Jason Hunter. See the cos-license.html file
434 1311 berkley
for details of the license.  Licensor retains title to and ownership of the
435 1307 jones
Software and all enhancements, modifications, and updates to the Software.
436 2441 jones
437 2599 jones
This software includes the JDBC driver for PostgreSQL.  See the
438
postgresql-license.txt file for details.