bio2rdf-svncommits Mailing List for bio2rdf (Page 9)
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From: <p_a...@us...> - 2009-11-19 01:28:23
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Revision: 792
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=792&view=rev
Author: p_ansell
Date: 2009-11-19 01:28:10 +0000 (Thu, 19 Nov 2009)
Log Message:
-----------
bump version number to 0.8.1 for release
Modified Paths:
--------------
trunk/build.xml
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From: <p_a...@us...> - 2009-11-19 01:27:24
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Revision: 791
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=791&view=rev
Author: p_ansell
Date: 2009-11-19 01:27:14 +0000 (Thu, 19 Nov 2009)
Log Message:
-----------
split uniprot licenses off from ebi general license page
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2009-11-19 01:19:47
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Revision: 790
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=790&view=rev
Author: p_ansell
Date: 2009-11-19 01:19:39 +0000 (Thu, 19 Nov 2009)
Log Message:
-----------
more updates... autogeneration of include stub providers and queries working
Modified Paths:
--------------
trunk/build.xml
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/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/namespaceproviders.jsp
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From: <p_a...@us...> - 2009-11-18 23:47:29
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Revision: 789
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=789&view=rev
Author: p_ansell
Date: 2009-11-18 23:47:23 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
make kegg_gene work
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2009-11-18 23:40:59
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Revision: 788
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=788&view=rev
Author: p_ansell
Date: 2009-11-18 23:40:48 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
make irefindex work
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...> - 2009-11-18 23:31:23
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Revision: 787
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=787&view=rev
Author: p_ansell
Date: 2009-11-18 23:31:17 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
make up a patched version of the templating code for people who insist on using unencoded plus signs, and unencoded slashes that are not meant to be path separators
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-queries-config.n3
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/Utilities.java
trunk/src/war/namespaceproviders.jsp
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From: <p_a...@us...> - 2009-11-18 20:32:41
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Revision: 786
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=786&view=rev
Author: p_ansell
Date: 2009-11-18 20:32:28 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
configuration changes to cleanup the profile system
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/namespaceproviders.jsp
trunk/src/war/profiles.jsp
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From: <p_a...@us...> - 2009-11-18 04:19:42
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Revision: 785
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=785&view=rev
Author: p_ansell
Date: 2009-11-18 04:19:35 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
add nextbio to the list of uniprot HTML redirect providers
Modified Paths:
--------------
trunk/build.xml
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/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
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From: <p_a...@us...> - 2009-11-10 02:34:27
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Revision: 784
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=784&view=rev
Author: p_ansell
Date: 2009-11-10 02:34:18 +0000 (Tue, 10 Nov 2009)
Log Message:
-----------
provider and query fixes to make unsafe queries available for any namespace, not practical to restrict the namespaces centrally
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...> - 2009-11-10 01:00:32
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Revision: 783
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=783&view=rev
Author: p_ansell
Date: 2009-11-10 01:00:25 +0000 (Tue, 10 Nov 2009)
Log Message:
-----------
add language tagging support to the HTML output, and fix up things so that the dbpedia endpoint won't be accidentally blacklisted because of 400 bad query errors that come because it doesn't URL encode its internal URI's, and hence we can't know exactly what to encode ourselves easily
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/StatisticsEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/templates/proptable.vm
trunk/src/war/serverstats.jsp
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From: <p_a...@us...> - 2009-11-06 07:29:54
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Revision: 782
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=782&view=rev
Author: p_ansell
Date: 2009-11-06 07:29:42 +0000 (Fri, 06 Nov 2009)
Log Message:
-----------
make cpath work better with biopax xref resolution queries to reduce the number of physical queries needed for forward and reverse queries
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/base-bio2rdf-rdfrules-config.n3
trunk/src/war/WEB-INF/src/bio2rdf_all_partial_common_uris.pipe
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/multifetch.jsp
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From: <p_a...@us...> - 2009-11-05 00:39:21
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Revision: 781
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=781&view=rev
Author: p_ansell
Date: 2009-11-05 00:39:08 +0000 (Thu, 05 Nov 2009)
Log Message:
-----------
editor broken again, but hopefully closer to working properly than it was before ironically
Modified Paths:
--------------
trunk/src/war/secured/configurationeditor/edit.jsp
trunk/src/war/secured/configurationeditor/show.jsp
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From: <p_a...@us...> - 2009-11-04 23:45:23
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Revision: 780
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=780&view=rev
Author: p_ansell
Date: 2009-11-04 23:45:13 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
get show.jsp working for lists
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/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Utilities.java
trunk/src/war/secured/configurationeditor/show.jsp
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From: <p_a...@us...> - 2009-11-04 10:08:34
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Revision: 779
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=779&view=rev
Author: p_ansell
Date: 2009-11-04 10:08:25 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
make DBpedia work properly
Modified Paths:
--------------
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/SparqlQueryCreator.java
trunk/src/war/bio2rdf.owl
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From: <p_a...@us...> - 2009-11-03 10:26:42
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Revision: 778
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=778&view=rev
Author: p_ansell
Date: 2009-11-03 10:26:35 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
update one side of the doi to spectrum position so that spectrums appear on the relevant DOI page
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...> - 2009-11-03 09:47:20
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Revision: 777
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=777&view=rev
Author: p_ansell
Date: 2009-11-03 09:47:12 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
update the query definitions so robots won't be blacklisted for following /linksns/ by the automated code
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
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From: <p_a...@us...> - 2009-11-03 09:46:16
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Revision: 776
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=776&view=rev
Author: p_ansell
Date: 2009-11-03 09:45:59 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
allow linksns as it is just as efficient as reverseconstruct, which is in use with a large number of namespaces currently
Modified Paths:
--------------
trunk/src/war/robots.txt
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From: <p_a...@us...> - 2009-11-03 09:06:15
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Revision: 775
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=775&view=rev
Author: p_ansell
Date: 2009-11-03 09:06:09 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
output the schema for QueryBundle's
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/QueryBundle.java
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2009-11-03 07:43:59
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Revision: 774
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=774&view=rev
Author: p_ansell
Date: 2009-11-03 07:43:48 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
add in support for a nmrshiftdb_bib namespace along with a rule and changes to the relevant 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-rdfrules-config.n3
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From: <p_a...@us...> - 2009-11-03 00:51:48
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Revision: 773
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=773&view=rev
Author: p_ansell
Date: 2009-11-03 00:51:39 +0000 (Tue, 03 Nov 2009)
Log Message:
-----------
add another provider in for doi using the nmrshiftdb endpoint, and add in support for the nmrshiftdb_peak namespace
Modified Paths:
--------------
trunk/build.xml
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-queries-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/web-production-template.xml
trunk/src/war/manualrefresh.jsp
Added Paths:
-----------
trunk/src/war/META-INF/context.xml
trunk/src/war/WEB-INF/test-simplest-configuration.n3
trunk/src/war/WEB-INF/web-production-template-qutesoe.xml
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From: <p_a...@us...> - 2009-10-29 03:47:43
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Revision: 772
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=772&view=rev
Author: p_ansell
Date: 2009-10-29 03:47:35 +0000 (Thu, 29 Oct 2009)
Log Message:
-----------
reduce logging level, add beginnings of label fetch and cache code and fix up the medicare provider code
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-rdfrules-config.n3
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/Utilities.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-10-29 01:50:56
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Revision: 771
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=771&view=rev
Author: p_ansell
Date: 2009-10-29 01:50:49 +0000 (Thu, 29 Oct 2009)
Log Message:
-----------
add medicare drugs provider
Modified Paths:
--------------
trunk/build.xml
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-queries-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-rdfrules-config.n3
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
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-10-26 05:27:53
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Revision: 770
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=770&view=rev
Author: p_ansell
Date: 2009-10-26 05:27:47 +0000 (Mon, 26 Oct 2009)
Log Message:
-----------
tag 0.8.0 version
Modified Paths:
--------------
tags/0.8.0/src/war/xsl-sources/geneid.xsl~
Added Paths:
-----------
tags/0.8.0/
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From: <p_a...@us...> - 2009-10-26 05:02:40
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Revision: 769
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=769&view=rev
Author: p_ansell
Date: 2009-10-26 05:02:25 +0000 (Mon, 26 Oct 2009)
Log Message:
-----------
rewrite profiles URL's
Modified Paths:
--------------
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/profiles.jsp
trunk/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2009-10-26 03:46:58
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Revision: 768
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=768&view=rev
Author: p_ansell
Date: 2009-10-26 03:46:52 +0000 (Mon, 26 Oct 2009)
Log Message:
-----------
add note in RdfFetchController about the place where I have to start when I want to include NamespaceEntry items into statistics
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
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