bio2rdf-svncommits Mailing List for bio2rdf (Page 21)
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From: <p_a...@us...> - 2009-05-26 05:57:56
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Revision: 492
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=492&view=rev
Author: p_ansell
Date: 2009-05-26 05:57:48 +0000 (Tue, 26 May 2009)
Log Message:
-----------
change over default to not try to import from rdf
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
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From: <p_a...@us...> - 2009-05-26 05:33:02
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Revision: 491
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=491&view=rev
Author: p_ansell
Date: 2009-05-26 05:32:54 +0000 (Tue, 26 May 2009)
Log Message:
-----------
get customquery import from rdf working
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.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/test-bio2rdf-configuration.n3
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From: <p_a...@us...> - 2009-05-26 04:12:22
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Revision: 490
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=490&view=rev
Author: p_ansell
Date: 2009-05-26 04:12:14 +0000 (Tue, 26 May 2009)
Log Message:
-----------
fix instances where the strings were being given with quotes, need to remember to use Value.stringValue() to get the unquoted version in future
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
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From: <p_a...@us...> - 2009-05-26 04:06:41
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Revision: 489
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=489&view=rev
Author: p_ansell
Date: 2009-05-26 04:06:33 +0000 (Tue, 26 May 2009)
Log Message:
-----------
add symboldotbio2rdfdotorg normalisation rule to diseasome as the erroneous URI's are used there as well
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-26 04:05:17
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Revision: 488
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=488&view=rev
Author: p_ansell
Date: 2009-05-26 04:05:10 +0000 (Tue, 26 May 2009)
Log Message:
-----------
more progress including configuration and rdf import for providerconfiguration partial success so far
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-05-26 02:22:15
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Revision: 487
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=487&view=rev
Author: p_ansell
Date: 2009-05-26 01:38:12 +0000 (Tue, 26 May 2009)
Log Message:
-----------
add inchi to the list of allowed unsafeconstruct namespaces due to its heavy use of + and / internally, which are both munged by percent encoding and urlunencoding
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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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:
-----------
make inchi rule a bit smarter
Modified Paths:
--------------
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:
-----------
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...> - 2009-05-25 11:05:17
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Revision: 484
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=484&view=rev
Author: p_ansell
Date: 2009-05-25 11:05:09 +0000 (Mon, 25 May 2009)
Log Message:
-----------
add more structure to the creation of ProviderConfiguration's from RDF
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
trunk/src/war/WEB-INF/test-bio2rdf-configuration.n3
trunk/src/war/WEB-INF/urlrewrite.xml
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From: <p_a...@us...> - 2009-05-25 06:42:18
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Revision: 483
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=483&view=rev
Author: p_ansell
Date: 2009-05-25 06:42:07 +0000 (Mon, 25 May 2009)
Log Message:
-----------
add mquter localised drugbank as the official endpoint was very unresponsive and it could be downloaded, and add reverseconstruct for gi, and fix iproclass reverse construct provider which was not actually used for reverseconstruct
Modified Paths:
--------------
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:
--------------
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:
-----------
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:
--------------
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 08:05:18
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Revision: 480
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=480&view=rev
Author: p_ansell
Date: 2009-05-23 08:05:10 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add test configuration file based on the current set of 0.6.0_pre features
Added Paths:
-----------
trunk/src/war/WEB-INF/test-bio2rdf-configuration.n3
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From: <p_a...@us...> - 2009-05-23 08:04:19
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Revision: 479
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=479&view=rev
Author: p_ansell
Date: 2009-05-23 08:04:11 +0000 (Sat, 23 May 2009)
Log Message:
-----------
first proof of concept for getting configuration from RDF with sesame and selecting the provider URI's from the configuration
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/ProviderConfiguration.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/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-05-23 06:19:55
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Revision: 478
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=478&view=rev
Author: p_ansell
Date: 2009-05-23 06:19:33 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add note about having to fix the order of the test strings, as it is important to the scheme
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
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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...> - 2009-05-23 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:
--------------
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 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:
--------------
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 04:47:07
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Revision: 474
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=474&view=rev
Author: p_ansell
Date: 2009-05-23 04:46:49 +0000 (Sat, 23 May 2009)
Log Message:
-----------
add new provider configuration parts
Modified Paths:
--------------
trunk/build.xml
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 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:
--------------
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:
-------------
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 02:22:42
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Revision: 472
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=472&view=rev
Author: p_ansell
Date: 2009-05-23 01:41:08 +0000 (Sat, 23 May 2009)
Log Message:
-----------
fix homologene html provider
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-22 10:11:24
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Revision: 471
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=471&view=rev
Author: p_ansell
Date: 2009-05-22 10:11:15 +0000 (Fri, 22 May 2009)
Log Message:
-----------
fix smart:sm to be recognised as smart:SM which actually has links, still to do normalisation rule for this
Modified Paths:
--------------
trunk/src/war/WEB-INF/urlrewrite.xml
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From: <p_a...@us...> - 2009-05-22 09:46:25
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Revision: 470
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=470&view=rev
Author: p_ansell
Date: 2009-05-22 09:46:24 +0000 (Fri, 22 May 2009)
Log Message:
-----------
add unists as reverse construct on geneid since it is very rarely actually available at unists.bio2rdf.org/sparql
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-05-22 09:13:03
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Revision: 469
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=469&view=rev
Author: p_ansell
Date: 2009-05-22 09:12:50 +0000 (Fri, 22 May 2009)
Log Message:
-----------
add some extra links and reverse construct providers
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/demo.rdf
trunk/src/war/index.html
trunk/src/war/mquter-index.html
trunk/src/war/quebec-index.html
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From: <p_a...@us...> - 2009-05-22 08:07:44
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Revision: 468
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=468&view=rev
Author: p_ansell
Date: 2009-05-22 08:07:37 +0000 (Fri, 22 May 2009)
Log Message:
-----------
increase pubmed discoverability using mesh and link pubmed to citations
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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