Project

General

Profile

metacat / README @ 3000

1
#
2
#  '$RCSfile$'
3
#   '$Author: jones $'
4
# '$Revision: 2975 $'
5
#     '$Date: 2006-04-03 03:54:47 -0700 (Mon, 03 Apr 2006) $'
6
#
7

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

    
11
Version: 1.5.0 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

    
28
Patch contributors:
29
              Andrea Chadden (chadden@nceas.ucsb.edu)
30
              Chris Jones (cjones@msi.ucsb.edu)
31
              Johnoel Ancheta (johnoel@hawaii.edu)
32
              Owen Jones (owen.jones@imperial.ac.uk)
33

    
34
Metacat is a flexible database storage system for XML formatted
35
documents and associated binary files. Metacat models the structure of the
36
XML document, therefore allowing storage of XML documents with arbitrary
37
schemas. Metacat supports several databases on the back-end, including Oracle,
38
PostgreSQL and SQL Server (limited).  The server supports XML document
39
storage, retrieval, query, validation, and transformation (using the XSLT
40
stylesheet language).  In addition, there is a mechanism for replicating the
41
database to other metacat instances for backup and load balancing purposes.
42
Metacat currently uses an LDAP database for authenticating users, but was
43
written to accomodate other authentication services as well.
44

    
45
Installation
46
------------
47
See the file "docs/user/metacatinstall.html" for detailed instructions.
48

    
49
Release Notes for 1.5.0:
50
------------------------
51

    
52
This release comes with performace improvement, user interface enhancements,
53
and bug fixes. Below is the list of bug fixes and performance improvements. 
54

    
55
Bug Fixes:
56
* Modify property values of harvester registration servlets to match the
57
  servlet-mapping URL values in web.xml. The old values used the servlet
58
  class names. This worked in Tomcat 4 but seems to break in Tomcat 5 on
59
  Windows. The new values use the servlet-mapping URL values. This should
60
  work in both Tomcat 4 and Tomcat 5. (Bug 162)
61
* Re-implement logic to prune old log entries from the HARVEST_LOG and
62
  HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint
63
  violations in the database because it tried to delete parent records from
64
  HARVEST_LOG prior to deleting child records from
65
  HARVEST_DETAIL_LOG. (Bug 162)
66
* In data registry, minor bugs fixed like the error page shows the link back
67
  to the form when error page was generated because of a document read
68
  request from search results page,  the successful delete button leading
69
  to a blank screen and the old ACL overwritten by the registry.
70
  (Bugs 1307, 1310, 1322, 1344, 1551)
71
* Changed the code to support insertion of following characters: ', `,
72
  charcters in the Numeric Character Reference format (&#xyz;) and
73
  characters like µ. Characters like µ will be converted to and stored in
74
  Numeric Character Reference format(&#xyz;). They will also be returned
75
  in Numeric Character Reference and it is upto the client to convert them
76
  and display them accordingly in the application. Partial fix provided by
77
  Johnoel Ancheta. (Bug 1538,1711)
78
* Spatial search failed on Oracle because of invalid entries made by
79
  some documents in the nodedata column of xml_nodes for paths involving
80
  'eastBoundingCoordinate', 'westBoundingCoordinate',
81
  'northBoundingCoordinate', 'southBoundingCoordinate'. A new column
82
  nodedatanumerical was added to xml_nodes table such that all the numerical
83
  nodedata is stored in this column and this column is now used for spatial
84
  search. (Bug 1703, 1718)
85
* In the default skin, clicking on the keywords on the home page did not
86
  result is a search being done. Fix provided by Owen Jones. (Bug 1768)
87
* Metacat generated a success message even when a document which didnt
88
  exsist was requested for deletion. This has been fixed. (Bug 1850)
89
* "packagetype" in xml-relation table was entered as eml200 namespace when
90
  an eml201 document was inserted. This is fixed now so that "packagetype"
91
  in xml-relation table points to eml201 namespace. (Bug 1979)
92
* System_id in xml_catalog pointed to http://knb.ecoinformatics.org/knb/
93
  earlier. Fixed such that it points to the locally installed metacat url. 
94
  (Bug 1986)
95
* Changes to the Query subsystem fix bugs that prevented attributes from 
96
  being expressed solely in the xpath query statement and the returnfield 
97
  values. For instance, a query URL may now include search strings like 
98
  '@packageId=sbclter%25' and return strings like 'returnfield=@packageId'.
99
  Previously, the attribute had to be appended to an element: 
100
  '/eml/@packageId=sbclter%25'. These fixes change DBQuery.java, 
101
  QuerySpecification.java, and QueryTerm.java (Bug 2052)
102
* Search query failed in case of Oracle if number of documents in the result
103
  were more than 1000. This has been fixed. (Bug 2000)
104
* Removed any occurence of enum which is now a keyword in Java 1.5
105

    
106

    
107
Enhancements:
108
* Major improvements done in user interface for the data registeries and
109
  various other skins. Improvements done based on suggestions from Mark
110
  Stromberg, Laura Downey and others. Improvements also done in resultset.xsl,
111
  the default skin and ldap templates. (Bug 1948)
112
* Coded added such that administrator can delete documents irrespective of
113
  who the document belongs to.
114
* Performance impovement done in searching of datasets. A part of the search
115
  time was taken up because of generation of resultset after the search had be
116
  done. So this was the sequence of events in earlier metacat
117
  1) Search for the given text
118
  2) A list of docids generated
119
  3) For each of the docids
120
     3a) Use xml_index and xml_nodes table to generate the string descibing
121
         the document including the returnfields requested in the search
122
  4) Add all the strings from step 3a to send back the resultant
123
     document. Here a decent amount of time was being taken by step 3a. 
124
  The algorithm is now modified by addition of two tables xml_queryresult and
125
  xml_returnfields and a user defined parameter xml_returnfield_count. The
126
  new algorithm works as follows:
127
  1) Search for the given text
128
  2) A list of docids is generated
129
  3) For the given set of return fields generate a unique string and check
130
     if that string exists in xml_returnfields
131
     3a) If string does not exist in xml_returnfield, then enter a new
132
         record usage_count as 1 and returnfield_string as the unique string
133
         generated above.
134
     3b) Else if the string exists, increment usage_count
135
  4) Given the docids from step 2 and the id of the returnfield record from
136
     step 3, query for any docids that already exist in xml_queryresult.
137
     For the docids that do exist, get the queryresult_string.
138
  5) For rest of the docids from step2 which were not found in step 4, do
139
     the following for each of the documents:
140
     5a) Use xml_index and xml_nodes table to generate the string descibing
141
         the document including the returnfields requested in the search
142
     5b) If usage_count of the record from step is more than
143
         xml_returnfield_count set in metacat.properties, then store the
144
         string in xml_queryresult as a record which has the returnfield_id
145
         representing the set of returnfields, docid representing the
146
         document and the string as queryresult_string.
147
  6) Add all the strings from step 4 and step 5a to send back the resultant
148
     document
149
  So the results from step 3a in previous algorithm are effectively cached
150
  and hence same computation is not done again and again for each search.
151
  When a document is deleted, all the entries for that document in
152
  xml_queryresult table are also deleted. When a document is updated, all
153
  the entries for that document in xml_queryresult table are deleted. This
154
  works fine because those entries will be generated and cached again the
155
  next time the document is part of a search is requested.
156
* Performance impovement done for % search.
157
* Following new functions added to metacat client API: a method to set access
158
  on an xml document and a method to get newest version for a given document.
159
* Implement a new HarvesterServlet for running Harvester as a servlet. This
160
  eliminates the need to run Harvester in a terminal window. By default, the
161
  HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user
162
  documentation will be modified to instruct Harvester administrators to
163
  uncomment the HarvesterServlet entry.
164
* Minor enhancement to support multiple email addresses for harvester
165
  administrator and site contact. Each address is separated by a comma or
166
  semicolon.
167
* Increase number of rows in Harvest List Editor from 300 to 1200.
168
* Changed default maxHarvests value to 0. Added logic to ignore maxHarvests
169
  value when it is set to 0 or a negative number. This allows Harvester to
170
  run indefinitely without shutting down after reaching a maximum number of
171
  harvests. The previous default value of 30 would cause Harvester to
172
  terminate after 30 harvests.
173

    
174
Details of all changes can be found in the bug database here:
175
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.5
176

    
177

    
178
Release Notes for 1.4.0:
179
------------------------
180

    
181
This is a major release, and is the first to introduce many new features to
182
Metacat.  Some of the major new features in this version of Metacat include:
183

    
184
* Added a new 'Harvester' that allows documents to be periodically pulled
185
  from distributed sources into metacat, useful for interfacing with other
186
  system types. See the Metacat Tour for details.
187
* Added new 'skins' capability to allow the GUI for the metacat web interface
188
  to be more easily customized to fit into site needs.  The skin is based on
189
  a flexible mix of XSLT, CSS, and Javascript.
190
* Added a web-based metadata entry form for submitting limited EML documents
191
  as part of a data registry.  The GUI for the registry is customizable and 
192
  is integrated with the 'skins' system for the main metacat interface.  The
193
  registry subsystem is written in Perl, and can simultaneously be used to 
194
  present multiple 'registry' interfaces.
195
* A new 'client API' has been developed and implemented in Java and in Perl 
196
  so that metacat functions can be accessed from any program in those
197
  languages.  The client API supports the major metacat servlet actions,
198
  including login(), logout(), query(), insert(), update(), delete(), and 
199
  upload(). See the Metacat Tour for details.
200
* Added a new 'getlog' action that produces a usage history for all major
201
  events.  So now an XML report can be generated for document reads, inserts,
202
  deletes, etc.  See the new section in the Metacat Tour.
203
* Added a new 'buildindex' action that can rebuild the index entries for any
204
  document in the database.
205
* The configuration file for metacat (metacat.properties) has been moved out
206
  of the jar file and into the WEB-INF directory, allowing far easier changes
207
  to the configuration parameters.
208
* Results in default web interface are sorted by title in the XSLT 
209
  (configurable)
210
* Many bugs were fixed.
211

    
212
Details of all changes can be found in the bug database here:
213
http://bugzilla.ecoinformatics.org/buglist.cgi?product=Metacat&target_milestone=1.4
214

    
215
Release Notes for 1.3.1:
216
------------------------
217

    
218
This is a simple interim bug fix. No major functionality changes. Bugs fixed 
219
include:
220
 1) Metacat 1.3.0 doesn't work in Java 1.3 because a subtle API differnce in 
221
    Java 1.3 and Java 1.4. Currently, Metacat 1.3.1 will work in both Java 1.3 
222
    and Java 1.4.
223
 2) Distribution package size was reduced.
224

    
225

    
226
Release Notes for 1.3.0
227
------------------------
228

    
229
In 1.3.0 release, the structure of the xml_access table was changed and a new
230
table, xml_accesssubtree was added. If you try to update a previously 
231
installed Metacat, you should run a script file to updated the table structure 
232
before installation.
233
For Oracle user: At the SQLPLUS prompt type the following -
234
@src/reviseformetacat13.sql
235
For Postgresql user: At install directory prompt type the following -
236
psql exp < src/reviseformetacat13_postgres.sql
237
(where 'exp' is the database name).
238

    
239
After installation, user should run "ant schemasql" command to register EML2
240
schema in xml_catalog table.
241

    
242
If you are a new Metacat user, this step is unneeded.
243

    
244
Note: 1) We recommend to use Tomcat 4 and JAVA 1.4 to run Metacat. Otherwise, 
245
         it will cause potential replication issues.
246
      2) Delete the xercesImpl.jar and xmlParserAPIs.jar files 
247
         which are in $CATALINA_HOME/common/endorsed. They are old version and
248
         don't support XML schema validation.
249

    
250
New Features in 1.3.0
251
  1) Partialy support EML2 document. User can store, query, read and write
252
     EML2 documents. However, Metacat only support access control in resource
253
     level. The subtree level access control will be ignored.
254
  2) Support other xml document base on namespace/schema.
255
  3) Support query for attribute value
256
  4) Assign MIME type to data file base on metadata when user try to read it.
257
  5) Owner can assign access rules to a document which does not have access 
258
     document to apply it.
259
  6) Support exporting single file, not only whole package
260
  7) Resupport Microsoft SQL Server.
261

    
262
Fixes in 1.3.0:
263
  1) Couldn't finish delta T replication for large set of documents.
264
  2) Couldn't create access control during delta T replication.
265
  3) Eorr will be written to a seperated log file if some documents
266
     were failed in replication.
267
  4) Decrease the time to create access rules during insert or update 
268
     a package.
269
     
270
Documentation
271
-------------
272
See the docs directory for detailed documentation and installation
273
instructions.
274

    
275
Details of the Metacat architecture can be found on the website for
276
the Knowledge Network for Biocomplexity (KNB):
277

    
278
  http://knb.ecoinformatics.org/software/metacat/
279

    
280
Contributions to this work are welcome.  Please see the above web site
281
for details on how to contribute.
282

    
283
Major Known Bugs or Feature Requests (see http://bugzilla.ecoinformatics.org)
284
-----------------------------------------------------------------------------
285
If you discover a bug please report it, either by email (above) or by using
286
our bug tracking system (http://bugzilla.ecoinformatics.org). There is a
287
list of currently unimplemented features in Bugzilla that we are working on
288
for the next release.
289

    
290
Legalese
291
--------
292
This software is copyrighted by The Regents of the University of California
293
and the National Center for Ecological Analysis and Synthesis
294
and licensed under the GNU GPL; see the 'LICENSE' file for
295
details.
296

    
297
This material is based upon work supported by the
298
National Science Foundation under Grant No. DEB99-80154, DBI99-04777, and
299
0225676 for SEEK.  Any opinions, findings and conclusions or recomendations 
300
expressed in this material are those of the author(s) and do not necessarily 
301
reflect the views of the National Science Foundation (NSF).
302

    
303
This software is partially supported by a grant from the Andrew W. 
304
Mellon Foundation.
305

    
306
This product includes software developed by the Apache Software
307
Foundation (http://www.apache.org/). See the LICENSE file in lib/apache
308
for details.
309

    
310
The source code, object code, and documentation in the com.oreilly.servlet
311
package is copyright and owned by Jason Hunter. See the cos-license.html file
312
for details of the license.  Licensor retains title to and ownership of the
313
Software and all enhancements, modifications, and updates to the Software.
314

    
315
This software includes the JDBC driver for PostgreSQL.  See the 
316
postgresql-license.txt file for details.