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bio2rdf-svncommits
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From: <p_a...@us...> - 2008-12-12 00:19:58
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Revision: 190
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=190&view=rev
Author: p_ansell
Date: 2008-12-12 00:19:54 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
move uri's in rdf rule class to static part and minor fix to properties file
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-20 00:08:38
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Revision: 225
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=225&view=rev
Author: p_ansell
Date: 2009-03-20 00:08:35 +0000 (Fri, 20 Mar 2009)
Log Message:
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add dailymed and drugbank rules and provider configs and add xmlEncoded_urlEncoded_ versions of input_X and queryString for use in RDF/XML templates
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-30 05:29:56
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Revision: 237
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=237&view=rev
Author: p_ansell
Date: 2009-03-30 05:29:46 +0000 (Mon, 30 Mar 2009)
Log Message:
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add Test URI's to ProviderConfigurations so that in future we can automate network analysis based on them
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-13 07:12:15
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Revision: 283
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=283&view=rev
Author: p_ansell
Date: 2009-04-13 07:12:14 +0000 (Mon, 13 Apr 2009)
Log Message:
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add lower/upper case functionality, only one provider enabled for one query so far
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-13 10:04:17
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Revision: 284
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=284&view=rev
Author: p_ansell
Date: 2009-04-13 10:04:16 +0000 (Mon, 13 Apr 2009)
Log Message:
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counttriplesfromlowercase and countlinksfromlowercase and avoid some issues with empty index lists in settings
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-14 10:48:58
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Revision: 290
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=290&view=rev
Author: p_ansell
Date: 2009-04-14 10:48:48 +0000 (Tue, 14 Apr 2009)
Log Message:
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fix .* to .+ so that /query/namespace: no longer matches against the query as someone seems to think it should according to logs but it shouldn't
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-17 02:08:26
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Revision: 295
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=295&view=rev
Author: p_ansell
Date: 2009-04-17 02:05:30 +0000 (Fri, 17 Apr 2009)
Log Message:
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add some more unsafe providers, including first providers for pchem
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-20 04:00:46
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Revision: 331
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=331&view=rev
Author: p_ansell
Date: 2009-04-20 04:00:42 +0000 (Mon, 20 Apr 2009)
Log Message:
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add NamespaceEntry in order to have http://bio2rdf.org/ns:NAMESPACE entries included in the /admin/configuration/rdfxml page
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
Added Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
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From: <p_a...@us...> - 2009-04-28 10:31:35
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Revision: 370
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=370&view=rev
Author: p_ansell
Date: 2009-04-28 10:31:22 +0000 (Tue, 28 Apr 2009)
Log Message:
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implement rule sorting and get most of myexperiment done
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-07 03:09:27
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Revision: 398
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=398&view=rev
Author: p_ansell
Date: 2009-05-07 03:09:15 +0000 (Thu, 07 May 2009)
Log Message:
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take out some long time hacks to fix bad data that sat in endpoints for large amounts of time, but now should be visible as it should be replaced
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-07 05:48:21
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Revision: 401
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=401&view=rev
Author: p_ansell
Date: 2009-05-07 05:48:20 +0000 (Thu, 07 May 2009)
Log Message:
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add geospecies, including fix so that endpointspecific elements are replaced on the endpoint URL template, as they are directly relevant to geospecies where we are just performing HTTP GET's
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-17 23:14:13
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Revision: 448
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=448&view=rev
Author: p_ansell
Date: 2009-05-17 23:14:04 +0000 (Sun, 17 May 2009)
Log Message:
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fix rule ordering so that the reverse order is used for output, so inputs are symmetrical with outputs
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/QueryBundle.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-23 02:51:13
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Revision: 473
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=473&view=rev
Author: p_ansell
Date: 2009-05-23 02:51:05 +0000 (Sat, 23 May 2009)
Log Message:
-----------
bump version and make only current branch a 0.5 version
Modified Paths:
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branches/0.5/build.xml
trunk/build.xml
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
Added Paths:
-----------
branches/0.5/
branches/0.5/src/war/WEB-INF/src/log4j.properties
branches/0.5/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/0.5/src/war/WEB-INF/urlrewrite.xml
branches/0.5/src/war/demo.rdf
branches/0.5/src/war/index.html
branches/0.5/src/war/mquter-index.html
branches/0.5/src/war/quebec-index.html
branches/0.5/src/war/robots.txt
Removed Paths:
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branches/0.4/
branches/0.5/src/war/WEB-INF/src/log4j.properties
branches/0.5/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/0.5/src/war/WEB-INF/urlrewrite.xml
branches/0.5/src/war/demo.rdf
branches/0.5/src/war/index.html
branches/0.5/src/war/mquter-index.html
branches/0.5/src/war/quebec-index.html
branches/0.5/src/war/robots.txt
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From: <p_a...@us...> - 2009-05-23 04:49:03
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Revision: 475
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=475&view=rev
Author: p_ansell
Date: 2009-05-23 04:48:53 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add some more
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
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From: <p_a...@us...> - 2009-05-23 05:40:01
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Revision: 476
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=476&view=rev
Author: p_ansell
Date: 2009-05-23 05:39:52 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add in some more parts that will be needed while the switch to RDF is made
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-23 06:15:59
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Revision: 477
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=477&view=rev
Author: p_ansell
Date: 2009-05-23 06:15:49 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add new attributes to the rdf output for provider configurations
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-06-22 03:06:29
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Revision: 560
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=560&view=rev
Author: p_ansell
Date: 2009-06-22 03:06:25 +0000 (Mon, 22 Jun 2009)
Log Message:
-----------
take test URI's out of RdfNormalisationRule class and make a one to many relationship between RuleTest and RdfNormalisationRule
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
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From: <p_a...@us...> - 2009-06-22 06:29:49
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Revision: 564
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=564&view=rev
Author: p_ansell
Date: 2009-06-22 06:29:48 +0000 (Mon, 22 Jun 2009)
Log Message:
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partially put profiles into the mix so they can be utilised with Rdf Rules at the applicable stages
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2009-07-01 01:06:42
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Revision: 602
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=602&view=rev
Author: p_ansell
Date: 2009-07-01 00:39:43 +0000 (Wed, 01 Jul 2009)
Log Message:
-----------
make things compile smoothly again, although implementation of HtmlPageRenderer is not yet complete
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2009-07-14 04:35:38
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Revision: 608
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=608&view=rev
Author: p_ansell
Date: 2009-07-14 04:35:29 +0000 (Tue, 14 Jul 2009)
Log Message:
-----------
add in relevant properties and change the settings helper methods to work with the improved profile matching abilities
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-07-27 04:40:46
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Revision: 638
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=638&view=rev
Author: p_ansell
Date: 2009-07-27 04:40:40 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
keep unrecognised statements in a memory buffer so that we don't lose them when the statement is unrecognised
any issues with URI renaming are implementation specific, this just ensures that they don't get lost through lack of a method for keeping them
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
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From: <p_a...@us...> - 2009-08-02 05:20:45
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Revision: 649
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=649&view=rev
Author: p_ansell
Date: 2009-08-02 05:20:37 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
some more extensive refactoring
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Bio2RdfContentNegotiator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/src/org/bio2rdf/HttpUrlQueryRunnable.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcherQueryRunnable.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/StatisticsEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
trunk/src/war/WEB-INF/src/org/bio2rdf/VelocityHelper.java
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From: <p_a...@us...> - 2009-08-02 05:45:50
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Revision: 650
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=650&view=rev
Author: p_ansell
Date: 2009-08-02 05:45:43 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
refactor RdfNormalisationRule and RuleTest along with related references to these classes
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/QueryBundle.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2009-08-12 04:21:43
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Revision: 671
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=671&view=rev
Author: p_ansell
Date: 2009-08-12 04:21:35 +0000 (Wed, 12 Aug 2009)
Log Message:
-----------
fix bug where the collection was supposed to be ordered, but wasn't being given implemented as a List
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
trunk/src/war/WEB-INF/src/org/bio2rdf/VoidUtility.java
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From: <p_a...@us...> - 2009-09-27 22:21:02
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Revision: 742
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=742&view=rev
Author: p_ansell
Date: 2009-09-27 22:20:55 +0000 (Sun, 27 Sep 2009)
Log Message:
-----------
add maxrows parameter to SPARQL queries
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/HttpUrlQueryRunnable.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcherSparqlQueryRunnable.java
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