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bio2rdf-svncommits
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From: <p_a...@us...> - 2008-10-22 10:21:44
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Revision: 138
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=138&view=rev
Author: p_ansell
Date: 2008-10-22 10:21:36 +0000 (Wed, 22 Oct 2008)
Log Message:
-----------
add debugging of which IP's are actually being sourced for given DNS addresses
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2008-11-03 05:16:32
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Revision: 153
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=153&view=rev
Author: p_ansell
Date: 2008-11-03 05:16:29 +0000 (Mon, 03 Nov 2008)
Log Message:
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fix url encoding issues and add tagging provider
Modified Paths:
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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/bio2rdf.properties
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From: <p_a...@us...> - 2008-11-27 02:23:31
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Revision: 179
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=179&view=rev
Author: p_ansell
Date: 2008-11-27 02:23:26 +0000 (Thu, 27 Nov 2008)
Log Message:
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fix countlinksns regex and lower logging levels and fix settings.toString(RepositoryConnection) so it uses the non-broken sesame rdf/xml writer
Modified Paths:
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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/bio2rdf.properties
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From: <p_a...@us...> - 2008-12-09 22:57:20
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Revision: 186
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=186&view=rev
Author: p_ansell
Date: 2008-12-09 22:57:16 +0000 (Tue, 09 Dec 2008)
Log Message:
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add a few sample neurocommons links for geneid, go, mesh and pubmed
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-10 04:55:16
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Revision: 209
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=209&view=rev
Author: p_ansell
Date: 2009-03-10 04:54:50 +0000 (Tue, 10 Mar 2009)
Log Message:
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adjust the pipes list and fix html providers configuration for uniprot
Modified Paths:
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trunk/src/war/WEB-INF/src/constructbio2rdf.pipe
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/src/pipes.list
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From: <p_a...@us...> - 2009-03-18 04:04:07
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Revision: 219
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=219&view=rev
Author: p_ansell
Date: 2009-03-18 04:03:51 +0000 (Wed, 18 Mar 2009)
Log Message:
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rename and fix pipe definition
Added Paths:
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trunk/src/war/WEB-INF/src/bio2rdf-basic.pipe
Removed Paths:
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trunk/src/war/WEB-INF/src/constructbio2rdf.pipe
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From: <p_a...@us...> - 2009-03-20 04:55:49
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Revision: 229
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=229&view=rev
Author: p_ansell
Date: 2009-03-20 04:55:44 +0000 (Fri, 20 Mar 2009)
Log Message:
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fix up taxonomy.bio2rdf.org/sparql rule
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-30 05:50:15
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Revision: 238
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=238&view=rev
Author: p_ansell
Date: 2009-03-30 05:50:10 +0000 (Mon, 30 Mar 2009)
Log Message:
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new pipes
Modified Paths:
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trunk/src/war/WEB-INF/src/pipes.list
Added Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_basic_from_uri.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators_citations.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators_citations_short.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing_from_uri.pipe
trunk/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml.pipe
trunk/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml_linksns_style.pipe
Removed Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
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From: <p_a...@us...> - 2009-04-13 01:56:37
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Revision: 279
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=279&view=rev
Author: p_ansell
Date: 2009-04-13 01:56:31 +0000 (Mon, 13 Apr 2009)
Log Message:
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add a similar version of the uri_rank using namespace and identifier parameters and move the uri version to _from_uri
Modified Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_uri_rank.pipe
Added Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_uri_rank_from_uri.pipe
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From: <p_a...@us...> - 2009-04-13 10:55:39
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Revision: 285
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=285&view=rev
Author: p_ansell
Date: 2009-04-13 10:55:35 +0000 (Mon, 13 Apr 2009)
Log Message:
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add more fromlowercase query types
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-04-18 08:36:18
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Revision: 310
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=310&view=rev
Author: p_ansell
Date: 2009-04-18 08:36:16 +0000 (Sat, 18 Apr 2009)
Log Message:
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add fix for endpointspecificness of query uri's as well as standard uri's
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
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...> - 2009-04-21 01:24:10
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Revision: 340
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=340&view=rev
Author: p_ansell
Date: 2009-04-21 01:24:02 +0000 (Tue, 21 Apr 2009)
Log Message:
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add some new ecocyc related pipes
Modified Paths:
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trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
Added Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_pr_tr_co_in_bi_ci_mesh.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_promoter_transcriptionunits.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_promoter_transcriptionunits_components.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites_citations.pipe
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From: <p_a...@us...> - 2009-05-01 07:52:10
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Revision: 378
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=378&view=rev
Author: p_ansell
Date: 2009-05-01 07:52:08 +0000 (Fri, 01 May 2009)
Log Message:
-----------
add new pipes
Added Paths:
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trunk/src/war/WEB-INF/src/bio2rdf_all_partial_common_uris.pipe
trunk/src/war/WEB-INF/src/bio2rdf_basic_from_multiple_uri.pipe
trunk/src/war/WEB-INF/src/bio2rdf_linkstonamespace_from_multiple_helper.pipe
trunk/src/war/WEB-INF/src/bio2rdf_multiple_by_namespace.pipe
trunk/src/war/WEB-INF/src/bio2rdf_ncbigi.pipe
trunk/src/war/WEB-INF/src/bio2rdf_partial_common_uris_by_namespace.pipe
trunk/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml_linkstonamespace_style.pipe
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From: <p_a...@us...> - 2009-05-07 11:36:23
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Revision: 408
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=408&view=rev
Author: p_ansell
Date: 2009-05-07 11:36:19 +0000 (Thu, 07 May 2009)
Log Message:
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fix taglabels being called for everything, and include a new static query to identify when a namespace is unknown
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
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
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From: <p_a...@us...> - 2009-05-07 12:03:19
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Revision: 409
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=409&view=rev
Author: p_ansell
Date: 2009-05-07 12:03:10 +0000 (Thu, 07 May 2009)
Log Message:
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add dnsonly query for users who want performance with a decrease in the amount of data that is accessible
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-11 22:45:33
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Revision: 433
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=433&view=rev
Author: p_ansell
Date: 2009-05-11 22:45:26 +0000 (Mon, 11 May 2009)
Log Message:
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fix unists html provider, as it was previously attached to data, and add log.isinfoenabled wrapper in contenttypenegotiator for efficiency
Modified Paths:
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trunk/src/war/WEB-INF/src/de/fuberlin/wiwiss/pubby/negotiation/ContentTypeNegotiator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-18 09:05:07
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Revision: 454
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=454&view=rev
Author: p_ansell
Date: 2009-05-18 09:04:59 +0000 (Mon, 18 May 2009)
Log Message:
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add some tcm normalisation rules
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-20 00:54:09
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Revision: 462
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=462&view=rev
Author: p_ansell
Date: 2009-05-20 00:32:40 +0000 (Wed, 20 May 2009)
Log Message:
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fix hubmed and log levels
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-23 23:16:01
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Revision: 481
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=481&view=rev
Author: p_ansell
Date: 2009-05-23 23:15:53 +0000 (Sat, 23 May 2009)
Log Message:
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add reverse construct for linkedct so it is browseable easily, and fix /links/pubmed issue that has been ignored by the database producers so far
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-24 06:29:32
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Revision: 482
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=482&view=rev
Author: p_ansell
Date: 2009-05-24 06:29:24 +0000 (Sun, 24 May 2009)
Log Message:
-----------
add some more rules and reduce logging level
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-26 01:14:45
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Revision: 485
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=485&view=rev
Author: p_ansell
Date: 2009-05-26 01:14:35 +0000 (Tue, 26 May 2009)
Log Message:
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make rdf.openmolecules.net RDF work by fixing the way documents are pulled into memory, was stripping line endings but really need to be adding them back again so that certain cases don't start failing
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
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From: <p_a...@us...> - 2009-05-26 02:18:41
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Revision: 486
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=486&view=rev
Author: p_ansell
Date: 2009-05-26 01:34:53 +0000 (Tue, 26 May 2009)
Log Message:
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make inchi rule a bit smarter
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-06-22 07:14:37
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Revision: 569
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=569&view=rev
Author: p_ansell
Date: 2009-06-22 07:14:36 +0000 (Mon, 22 Jun 2009)
Log Message:
-----------
lower some debugging levels
Modified Paths:
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trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
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From: <p_a...@us...> - 2009-06-24 02:19:19
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Revision: 585
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=585&view=rev
Author: p_ansell
Date: 2009-06-24 01:53:29 +0000 (Wed, 24 Jun 2009)
Log Message:
-----------
track down the bug, and leave a note to fix it
Modified Paths:
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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/RdfFetchController.java
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From: <p_a...@us...> - 2009-08-12 00:21:46
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Revision: 668
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=668&view=rev
Author: p_ansell
Date: 2009-08-12 00:21:40 +0000 (Wed, 12 Aug 2009)
Log Message:
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performance improvements facilitated by using Collection where possible and only using List where order is important
Modified Paths:
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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/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/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/Utilities.java
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