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From: <p_a...@us...> - 2010-05-11 04:23:51
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Revision: 867
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=867&view=rev
Author: p_ansell
Date: 2010-05-11 04:23:45 +0000 (Tue, 11 May 2010)
Log Message:
-----------
fix up the schema generation so it is non-static
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/ProvenanceRecord.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/RegexNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/StatisticsEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Template.java
trunk/src/war/WEB-INF/src/org/queryall/NormalisationRule.java
trunk/src/war/WEB-INF/src/org/queryall/RdfCompatible.java
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2010-05-11 00:07:26
|
Revision: 866
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=866&view=rev
Author: p_ansell
Date: 2010-05-11 00:07:19 +0000 (Tue, 11 May 2010)
Log Message:
-----------
fix some issues with the way normalisation rules were being parsed and output to RDF so that version 2 will work properly, but version 3 is now the default for the package
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/RegexNormalisationRule.java
trunk/src/war/WEB-INF/src/org/queryall/NormalisationRule.java
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From: <p_a...@us...> - 2010-05-10 04:36:59
|
Revision: 865
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=865&view=rev
Author: p_ansell
Date: 2010-05-10 04:36:53 +0000 (Mon, 10 May 2010)
Log Message:
-----------
minor fixes to make rule testing and namespace providers pages work again and add reverse construct source for mint namespace
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/namespaceproviders.jsp
trunk/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2010-05-07 05:12:55
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Revision: 864
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=864&view=rev
Author: p_ansell
Date: 2010-05-07 05:12:49 +0000 (Fri, 07 May 2010)
Log Message:
-----------
fix up some more errors and add the regex type URI to each of the current normalisation rules
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/RegexNormalisationRule.java
trunk/src/war/WEB-INF/src/org/queryall/NormalisationRule.java
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From: <p_a...@us...> - 2010-05-07 03:43:40
|
Revision: 863
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=863&view=rev
Author: p_ansell
Date: 2010-05-07 03:43:32 +0000 (Fri, 07 May 2010)
Log Message:
-----------
fix up references in jsp files that weren't included in the compile
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
trunk/src/war/WEB-INF/src/org/queryall/NormalisationRule.java
trunk/src/war/debug-configuration.jsp
trunk/src/war/internalschema.jsp
trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
trunk/src/war/namespaceproviders.jsp
trunk/src/war/profiles.jsp
trunk/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2010-05-07 03:33:49
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Revision: 862
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=862&view=rev
Author: p_ansell
Date: 2010-05-07 03:33:43 +0000 (Fri, 07 May 2010)
Log Message:
-----------
reform the way NormalisationRule's are implemented, only compiles so far, no testing performed
MAY BE BROKEN
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/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/bio2rdf.properties
trunk/src/war/debug-configuration.jsp
trunk/src/war/internalschema.jsp
trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
trunk/src/war/namespaceproviders.jsp
trunk/src/war/profiles.jsp
trunk/src/war/test-regexmethods.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/RegexNormalisationRule.java
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlNormalisationRule.java
trunk/src/war/WEB-INF/src/org/queryall/NormalisationRule.java
Removed Paths:
-------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
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From: <p_a...@us...> - 2010-04-30 22:10:03
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Revision: 861
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=861&view=rev
Author: p_ansell
Date: 2010-04-30 22:09:55 +0000 (Fri, 30 Apr 2010)
Log Message:
-----------
add cu.ns.bio2rdf.org/sparql back into the configuration
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2010-04-29 05:55:45
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Revision: 860
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=860&view=rev
Author: p_ansell
Date: 2010-04-29 05:55:39 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
update dbpedia rights URL
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-licenses-config.n3
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From: <p_a...@us...> - 2010-04-29 05:45:40
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Revision: 859
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=859&view=rev
Author: p_ansell
Date: 2010-04-29 05:45:34 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
make RESET_ENDPOINT_FAILURES_ON_SUCCESS work
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2010-04-29 04:29:01
|
Revision: 858
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=858&view=rev
Author: p_ansell
Date: 2010-04-29 04:28:55 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
add more ontology conditions on for the normalisation rule schema
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
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From: <p_a...@us...> - 2010-04-29 04:14:41
|
Revision: 857
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=857&view=rev
Author: p_ansell
Date: 2010-04-29 04:14:35 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
put labels on each of the predicates relating to rdf normalisation rules
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
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From: <p_a...@us...> - 2010-04-29 03:54:00
|
Revision: 856
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=856&view=rev
Author: p_ansell
Date: 2010-04-29 03:53:54 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
remove extra header lines on schema page
Modified Paths:
--------------
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2010-04-29 03:41:54
|
Revision: 855
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=855&view=rev
Author: p_ansell
Date: 2010-04-29 03:41:48 +0000 (Thu, 29 Apr 2010)
Log Message:
-----------
fix a few bugs, including /queryall/ that wasn't previously working
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-html-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-licenses-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/redirectToId.jsp
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From: <p_a...@us...> - 2010-04-20 01:23:45
|
Revision: 854
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=854&view=rev
Author: p_ansell
Date: 2010-04-20 01:23:39 +0000 (Tue, 20 Apr 2010)
Log Message:
-----------
add deletion rule for /countlinks/ operations to automagically remove zero value results so that actual results are easier to identify
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-html-config.n3
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
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2010-04-20 00:51:18
|
Revision: 853
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=853&view=rev
Author: p_ansell
Date: 2010-04-20 00:51:12 +0000 (Tue, 20 Apr 2010)
Log Message:
-----------
add release namespace, and tune up the uniparc provider
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-namespaceentries-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2010-04-19 22:47:16
|
Revision: 852
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=852&view=rev
Author: p_ansell
Date: 2010-04-19 22:47:10 +0000 (Mon, 19 Apr 2010)
Log Message:
-----------
change description on new rule
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
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From: <p_a...@us...> - 2010-04-19 22:34:44
|
Revision: 851
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=851&view=rev
Author: p_ansell
Date: 2010-04-19 22:34:37 +0000 (Mon, 19 Apr 2010)
Log Message:
-----------
add fixes for affymetrix taxon for homo sapiens and make it possible to resolve some affymetrix_resource items while still normalising the rest of the information by taking out the forward normalisation part of the hash to colon rule and making it a separate rule
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
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From: <p_a...@us...> - 2010-04-19 08:49:18
|
Revision: 850
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=850&view=rev
Author: p_ansell
Date: 2010-04-19 08:49:12 +0000 (Mon, 19 Apr 2010)
Log Message:
-----------
update some providers and queries, and make global change in the ecocyc rdfisers
Modified Paths:
--------------
trunk/src/util/python/ecocyc-dnabindsites2rdf.py
trunk/src/util/python/ecocyc-genelinks2rdf.py
trunk/src/util/python/ecocyc-genes2rdf.py
trunk/src/util/python/ecocyc-pathways2rdf.py
trunk/src/util/python/ecocyc-promoters2rdf.py
trunk/src/util/python/ecocyc-proteinfeatures2rdf.py
trunk/src/util/python/ecocyc-proteins2rdf.py
trunk/src/util/python/ecocyc-regulation2rdf.py
trunk/src/util/python/ecocyc-regulons2rdf.py
trunk/src/util/python/ecocyc-transunits2rdf.py
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-html-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2010-04-19 03:41:07
|
Revision: 849
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=849&view=rev
Author: p_ansell
Date: 2010-04-19 03:41:01 +0000 (Mon, 19 Apr 2010)
Log Message:
-----------
update pubmed rdfiser, and add new rule in to fix issue with pubmed rdfiser
Modified Paths:
--------------
trunk/src/war/WEB-INF/autogenerated-bio2rdf-query-insert-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-licenses-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
trunk/src/war/xsl-sources/pubmed.xsl
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From: <p_a...@us...> - 2010-04-15 22:18:58
|
Revision: 848
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=848&view=rev
Author: p_ansell
Date: 2010-04-15 22:18:52 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
add pubmed notice file that is required by NLM for Pubmed
Added Paths:
-----------
trunk/src/war/pubmed_notice_2010-04-09.html
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From: <p_a...@us...> - 2010-04-15 04:25:20
|
Revision: 847
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=847&view=rev
Author: p_ansell
Date: 2010-04-15 04:25:14 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
modify some providers
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-namespaceentries-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-html-config.n3
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From: <p_a...@us...> - 2010-04-14 04:58:50
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Revision: 846
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=846&view=rev
Author: p_ansell
Date: 2010-04-14 04:58:44 +0000 (Wed, 14 Apr 2010)
Log Message:
-----------
make the license work for irefindex
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-licenses-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
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From: <p_a...@us...> - 2010-04-14 04:28:21
|
Revision: 845
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=845&view=rev
Author: p_ansell
Date: 2010-04-14 04:28:15 +0000 (Wed, 14 Apr 2010)
Log Message:
-----------
add profile list to the html pages to make it easier to debug foreign configurations using the documents that it produces
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2010-04-14 04:00:35
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Revision: 844
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=844&view=rev
Author: p_ansell
Date: 2010-04-14 04:00:29 +0000 (Wed, 14 Apr 2010)
Log Message:
-----------
reduce logging level again
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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From: <p_a...@us...> - 2010-04-14 03:56:26
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Revision: 843
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=843&view=rev
Author: p_ansell
Date: 2010-04-14 03:56:19 +0000 (Wed, 14 Apr 2010)
Log Message:
-----------
change license system so that it doesn't use redirects, and hence RDF clients can discover the license URL directly in RDF documents
Modified Paths:
--------------
trunk/src/war/WEB-INF/autogenerated-bio2rdf-query-insert-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-licenses-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
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/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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