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From: <p_a...@us...> - 2009-08-10 23:20:42
|
Revision: 667
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=667&view=rev
Author: p_ansell
Date: 2009-08-10 23:20:36 +0000 (Mon, 10 Aug 2009)
Log Message:
-----------
add some basic introductory Void translation functionality
aim to make void models translateable into Bio2RDF Providers/Queries/Namespaces... but first off it would be nice to have Providers
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
trunk/src/war/error-sesame-output.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/VoidUtility.java
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From: <p_a...@us...> - 2009-08-10 01:18:16
|
Revision: 666
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=666&view=rev
Author: p_ansell
Date: 2009-08-10 01:18:05 +0000 (Mon, 10 Aug 2009)
Log Message:
-----------
update statistics functionality so that we can distinguish between software versions used to submit statistics, and centralise creation of SimpleDateFormat objects... would use a final static but SimpleDateFormat isn't threadsafe!
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/src/org/bio2rdf/StatisticsEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
trunk/src/war/atlas2rdf.jsp
trunk/src/war/errorstats.jsp
trunk/src/war/serverstats.jsp
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From: <p_a...@us...> - 2009-08-09 22:06:21
|
Revision: 665
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=665&view=rev
Author: p_ansell
Date: 2009-08-09 22:06:13 +0000 (Sun, 09 Aug 2009)
Log Message:
-----------
fix error stats total query time displayed values and add isPageable model support to CustomQuery's
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/errorstats.jsp
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From: <p_a...@us...> - 2009-08-09 06:03:54
|
Revision: 664
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=664&view=rev
Author: p_ansell
Date: 2009-08-09 06:03:42 +0000 (Sun, 09 Aug 2009)
Log Message:
-----------
add isPageable support to configuration file and fix namespace on a provider because it no longer exists
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
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From: <p_a...@us...> - 2009-08-06 09:02:58
|
Revision: 663
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=663&view=rev
Author: p_ansell
Date: 2009-08-06 09:02:50 +0000 (Thu, 06 Aug 2009)
Log Message:
-----------
improve the way the links are shown, and fix some providers that really required explicit pageoffset, and allow the plain pageoffset integer value to be put into the provider template
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/includes-css/html_page_styles.css
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From: <p_a...@us...> - 2009-08-06 08:27:27
|
Revision: 662
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=662&view=rev
Author: p_ansell
Date: 2009-08-06 08:27:20 +0000 (Thu, 06 Aug 2009)
Log Message:
-----------
add paging support to the interface if it is detected to be likely available... only enabled currently for simple ns:id queries, and restricted to showing up links to the first 20 page offsets
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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/bio2rdf.properties
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/atlas2rdf.jsp
trunk/src/war/debug-configuration.jsp
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2009-08-05 23:31:08
|
Revision: 661
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=661&view=rev
Author: p_ansell
Date: 2009-08-05 23:30:47 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
add drugbank provider to the quebecdnsonly profile so that elementary resolutions are possible
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
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From: <p_a...@us...> - 2009-08-04 01:20:56
|
Revision: 660
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=660&view=rev
Author: p_ansell
Date: 2009-08-04 01:20:50 +0000 (Tue, 04 Aug 2009)
Log Message:
-----------
add backwards compatibility check for old namespace title attribute
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
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From: <p_a...@us...> - 2009-08-04 00:44:18
|
Revision: 659
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=659&view=rev
Author: p_ansell
Date: 2009-08-04 00:44:11 +0000 (Tue, 04 Aug 2009)
Log Message:
-----------
create tag for 0.7.0 release version
Modified Paths:
--------------
tags/0.7.0/src/war/xsl-sources/geneid.xsl~
Added Paths:
-----------
tags/0.7.0/
tags/0.7.0/README
tags/0.7.0/build.xml
tags/0.7.0/buildlibs/
tags/0.7.0/dist/
tags/0.7.0/docs/
tags/0.7.0/gpl-v2.0.txt
tags/0.7.0/gpl-v3.txt
tags/0.7.0/src/
Removed Paths:
-------------
tags/0.7.0/README
tags/0.7.0/build.xml
tags/0.7.0/buildlibs/
tags/0.7.0/dist/
tags/0.7.0/docs/
tags/0.7.0/gpl-v2.0.txt
tags/0.7.0/gpl-v3.txt
tags/0.7.0/src/
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From: <p_a...@us...> - 2009-08-04 00:03:19
|
Revision: 658
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=658&view=rev
Author: p_ansell
Date: 2009-08-04 00:03:07 +0000 (Tue, 04 Aug 2009)
Log Message:
-----------
remove some providers that have been giving errors consistently
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-namespaceentries-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2009-08-03 23:39:26
|
Revision: 657
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=657&view=rev
Author: p_ansell
Date: 2009-08-03 23:39:18 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
bump to 0.7.0 release
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/templates/proptable.vm
trunk/src/war/debug-configuration.jsp
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From: <p_a...@us...> - 2009-08-03 04:20:46
|
Revision: 656
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=656&view=rev
Author: p_ansell
Date: 2009-08-03 04:20:38 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
fix serverstats.jsp regression
Modified Paths:
--------------
trunk/src/war/serverstats.jsp
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From: <p_a...@us...> - 2009-08-03 04:07:37
|
Revision: 655
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=655&view=rev
Author: p_ansell
Date: 2009-08-03 04:07:26 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
make up the error page for resources that don't exist or aren't available somehow
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/atlas2rdf.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/templates/error.vm
Removed Paths:
-------------
trunk/src/war/WEB-INF/templates/404.vm
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From: <p_a...@us...> - 2009-08-03 03:05:00
|
Revision: 654
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=654&view=rev
Author: p_ansell
Date: 2009-08-03 03:04:52 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
change definitions for prosite endpoint as it has been migrated back to the normalised URI scheme, and attempt to avoid titles if they are empty
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/includes-css/html_page_styles.css
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From: <p_a...@us...> - 2009-08-03 02:14:41
|
Revision: 653
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=653&view=rev
Author: p_ansell
Date: 2009-08-03 01:44:38 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
avoid outputting endpoint information unless we are actually wanting to log it so that the mature mirrors can avoid it and still have info level debugging enabled
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.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/bio2rdf.properties
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/WEB-INF/templates/page.vm
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/atlas2rdf.jsp
trunk/src/war/multifetch.jsp
trunk/src/war/redirectToId.jsp
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From: <p_a...@us...> - 2009-08-02 08:56:50
|
Revision: 652
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=652&view=rev
Author: p_ansell
Date: 2009-08-02 08:56:38 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
remove references to conn.getResponseCode() to avoid issues with accessing conn when it is in an error state
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
trunk/src/war/error-sesame-output.jsp
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From: <p_a...@us...> - 2009-08-02 08:28:37
|
Revision: 651
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=651&view=rev
Author: p_ansell
Date: 2009-08-02 08:28:31 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
reverse some previous changes... and try to figure out why the timeout takes twice as long as configured to get a connectexception and fail
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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/RdfFetcher.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.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
trunk/src/war/error-sesame-output.jsp
trunk/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2009-08-02 05:45:50
|
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...> - 2009-08-02 05:20:45
|
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 01:50:30
|
Revision: 648
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=648&view=rev
Author: p_ansell
Date: 2009-08-02 01:50:23 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
refactor all utility methods into one class from Settings and SparqlQueryCreator
Modified Paths:
--------------
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/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.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/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/atlas2rdf.jsp
trunk/src/war/debug-configuration.jsp
trunk/src/war/errorstats.jsp
trunk/src/war/internalschema.jsp
trunk/src/war/jsp-bio2rdf/kegg-search-http2rdf.jsp
trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
trunk/src/war/jsp-bio2rdf/sindice-search2rdf.jsp
trunk/src/war/jsp-bio2rdf/swoogle-search2rdf.jsp
trunk/src/war/jsp-bio2rdf/uniprot-search-http2rdf.jsp
trunk/src/war/multifetch.jsp
trunk/src/war/redirectToId.jsp
trunk/src/war/secured/configurationeditor/create_new.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
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From: <p_a...@us...> - 2009-08-02 01:19:27
|
Revision: 647
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=647&view=rev
Author: p_ansell
Date: 2009-08-02 01:19:20 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
extensive refactoring of the way querybundles and threads are created, and turn rdffetchcontroller into a useful object on its own
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-namespaceentries-config.n3
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/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-08-01 07:59:08
|
Revision: 646
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=646&view=rev
Author: p_ansell
Date: 2009-08-01 07:59:00 +0000 (Sat, 01 Aug 2009)
Log Message:
-----------
allow alternative namespace prefixes
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-namespaceentries-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
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From: <p_a...@us...> - 2009-08-01 07:04:35
|
Revision: 645
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=645&view=rev
Author: p_ansell
Date: 2009-08-01 07:04:20 +0000 (Sat, 01 Aug 2009)
Log Message:
-----------
fix behaviour of default providers so they have to be assigned to queries before they respond
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
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/templates/endpoints.vm
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From: <p_a...@us...> - 2009-07-30 23:08:59
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Revision: 644
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=644&view=rev
Author: p_ansell
Date: 2009-07-30 23:08:53 +0000 (Thu, 30 Jul 2009)
Log Message:
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convert profiles to the new set of reverse construct query types
Modified Paths:
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trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <p_a...@us...> - 2009-07-30 23:00:39
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Revision: 643
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=643&view=rev
Author: p_ansell
Date: 2009-07-30 23:00:32 +0000 (Thu, 30 Jul 2009)
Log Message:
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create primary and secondary reverseconstruct versions
Modified Paths:
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trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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