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From: <p_a...@us...> - 2008-10-02 23:16:08
|
Revision: 117
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=117&view=rev
Author: p_ansell
Date: 2008-10-02 23:15:58 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
fix html forwarding bug
Modified Paths:
--------------
trunk/build.xml
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...> - 2008-10-02 11:50:33
|
Revision: 116
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=116&view=rev
Author: p_ansell
Date: 2008-10-02 11:50:25 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
change the name of the distributed archives don't include minimal anymore
Modified Paths:
--------------
trunk/build.xml
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From: <p_a...@us...> - 2008-10-02 11:20:07
|
Revision: 115
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=115&view=rev
Author: p_ansell
Date: 2008-10-02 11:19:59 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
add a new rule and fix atlas2rdf.jsp with its blacklist functionality
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-10-02 07:07:48
|
Revision: 114
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=114&view=rev
Author: p_ansell
Date: 2008-10-02 07:07:38 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
add some error handling for bad endpoints that is persistent across the session
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...> - 2008-10-02 06:28:43
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Revision: 113
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=113&view=rev
Author: p_ansell
Date: 2008-10-02 06:28:38 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
update things so that regex works, and there is some error detection that is useful for the index queries particularly
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-10-02 03:43:06
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Revision: 112
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=112&view=rev
Author: p_ansell
Date: 2008-10-02 03:43:02 +0000 (Thu, 02 Oct 2008)
Log Message:
-----------
commit current progress in getting regex integrated
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-10-01 10:02:06
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Revision: 111
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=111&view=rev
Author: p_ansell
Date: 2008-10-01 10:01:49 +0000 (Wed, 01 Oct 2008)
Log Message:
-----------
add in regex, although it is not currently working for some reason
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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/atlas2rdf.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/QueryBundle.java
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From: <p_a...@us...> - 2008-10-01 08:24:12
|
Revision: 110
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=110&view=rev
Author: p_ansell
Date: 2008-10-01 08:24:08 +0000 (Wed, 01 Oct 2008)
Log Message:
-----------
commit just before adding the idea of a querybundle in order to support the configuration based normalisation rules
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/SparqlQueryCreator.java
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-10-01 07:26:33
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Revision: 109
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=109&view=rev
Author: p_ansell
Date: 2008-10-01 07:26:27 +0000 (Wed, 01 Oct 2008)
Log Message:
-----------
add randomising behaviour properly
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...> - 2008-10-01 06:57:40
|
Revision: 108
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=108&view=rev
Author: p_ansell
Date: 2008-10-01 06:57:36 +0000 (Wed, 01 Oct 2008)
Log Message:
-----------
generalise the process for any query, with an escape point for the first success
Modified Paths:
--------------
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-10-01 05:51:24
|
Revision: 107
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=107&view=rev
Author: p_ansell
Date: 2008-10-01 05:51:14 +0000 (Wed, 01 Oct 2008)
Log Message:
-----------
update some things to get some REGEX rule stuff going in the configuration and enable debugging support
Modified Paths:
--------------
trunk/build.xml
trunk/src/util/perl/cleanupdata.pl
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
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
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From: <p_a...@us...> - 2008-09-25 06:29:40
|
Revision: 106
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=106&view=rev
Author: p_ansell
Date: 2008-09-25 06:29:31 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
add in some fixes to various elements
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-09-25 00:34:27
|
Revision: 105
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=105&view=rev
Author: p_ansell
Date: 2008-09-25 00:34:18 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
move current version to the trunk
Added Paths:
-----------
trunk/
Removed Paths:
-------------
branches/stripped-down-version/
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From: <p_a...@us...> - 2008-09-25 00:31:22
|
Revision: 104
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=104&view=rev
Author: p_ansell
Date: 2008-09-25 00:31:13 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
fix the index and links queries to be objects instead of subjects of their respective RDF statements and bump build.xml version up to next release number
Modified Paths:
--------------
branches/stripped-down-version/build.xml
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2008-09-24 06:40:54
|
Revision: 103
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=103&view=rev
Author: p_ansell
Date: 2008-09-24 06:40:46 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
add some more providers to the properties file
Modified Paths:
--------------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2008-09-24 06:28:13
|
Revision: 102
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=102&view=rev
Author: p_ansell
Date: 2008-09-24 06:28:10 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
fix another bug
Modified Paths:
--------------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
branches/stripped-down-version/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-09-24 06:14:44
|
Revision: 101
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=101&view=rev
Author: p_ansell
Date: 2008-09-24 06:14:34 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
more refactoring
Modified Paths:
--------------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
branches/stripped-down-version/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-09-24 05:49:59
|
Revision: 100
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=100&view=rev
Author: p_ansell
Date: 2008-09-24 05:49:45 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
fix one small bug
Modified Paths:
--------------
branches/stripped-down-version/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-09-24 05:29:35
|
Revision: 99
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=99&view=rev
Author: p_ansell
Date: 2008-09-24 05:29:28 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
refactor atlas2rdf.jsp
Modified Paths:
--------------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/Settings.java
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/stripped-down-version/src/war/atlas2rdf.jsp
Added Paths:
-----------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2008-09-23 07:04:27
|
Revision: 98
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=98&view=rev
Author: p_ansell
Date: 2008-09-23 07:04:17 +0000 (Tue, 23 Sep 2008)
Log Message:
-----------
update package to utilise current endpoints by default and avoid some issues with redirecting when there is no default provider defined
Modified Paths:
--------------
branches/stripped-down-version/build.xml
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/stripped-down-version/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2008-09-18 15:27:29
|
Revision: 97
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=97&view=rev
Author: p_ansell
Date: 2008-09-18 22:27:38 +0000 (Thu, 18 Sep 2008)
Log Message:
-----------
update the compatibility with the new DNS methods
Modified Paths:
--------------
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/stripped-down-version/src/war/atlas2rdf.jsp
branches/stripped-down-version/src/war/xsl-sources/geneid.xsl
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From: <p_a...@us...> - 2008-09-11 01:25:30
|
Revision: 96
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=96&view=rev
Author: p_ansell
Date: 2008-09-11 01:25:39 +0000 (Thu, 11 Sep 2008)
Log Message:
-----------
add some more ignores and delete temporary files
Removed Paths:
-------------
branches/stripped-down-version/src/util/perl/bio-tab2rdf.pl~
branches/stripped-down-version/src/util/perl/cleanupdata.pl~
branches/stripped-down-version/src/util/perl/elmo.pl~
branches/stripped-down-version/src/util/perl/hgnc-csv2rdf.pl~
branches/stripped-down-version/src/util/perl/loadvirtuoso.pl~
branches/stripped-down-version/src/util/perl/mysql2sesame.pl~
branches/stripped-down-version/src/util/perl/regulondb-tab2rdf.pl~
branches/stripped-down-version/src/util/perl/regulondb-virtuoso.pl~
branches/stripped-down-version/src/util/shell/load_ttl.sh~
Property Changed:
----------------
branches/stripped-down-version/src/util/perl/
branches/stripped-down-version/src/util/shell/
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From: <p_a...@us...> - 2008-09-11 00:53:06
|
Revision: 95
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=95&view=rev
Author: p_ansell
Date: 2008-09-11 00:53:14 +0000 (Thu, 11 Sep 2008)
Log Message:
-----------
fix temporary file addition, and modify properties so that it doesn't happen again
Removed Paths:
-------------
branches/stripped-down-version/src/war/jsp-bio2rdf/bio2rdf-demo.rdf~
branches/stripped-down-version/src/war/jsp-bio2rdf/bio2rdf-header2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/biopax-xref2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/biopax2bpl-v1.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/biopax2bpl.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/construct-synonyme2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ensembl-g2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ensembl-p2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ensembl-t2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/fulltext2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/gdb-http2bio2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/go-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/hugo-http2bio2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/kegg-composite2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/kegg-kgml2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/kegg-kgml2rdf.xsl~
branches/stripped-down-version/src/war/jsp-bio2rdf/kegg-search-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/lsid-bio2rdf2lsid.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/lsid-sameas2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/mysql2statistics.rdf~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-entrez2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-genbank2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-geneid2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-gi-genbank2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-map-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-mesh-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-omim2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-pubchem2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/ncbi-pubmed2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/obo-xref2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/obo2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/pdb-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/reactome-taxon-all-http2seealso.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/reactome-taxon-http2seealso.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/reactome-xref2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/reactome2bio2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/search-rdfdata.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/search-v1.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/search.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/swoogle-search2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/uniprot-header2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/uniprot-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/uniprot-keyword-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/uniprot-rdf2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/uniprot-search-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/wsdl-authority.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/wsdl-service.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/wsdl-service2rdf.jsp~
Property Changed:
----------------
branches/stripped-down-version/src/war/jsp-bio2rdf/
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From: <p_a...@us...> - 2008-09-11 00:50:22
|
Revision: 94
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=94&view=rev
Author: p_ansell
Date: 2008-09-11 00:50:31 +0000 (Thu, 11 Sep 2008)
Log Message:
-----------
add some new things
Modified Paths:
--------------
branches/stripped-down-version/src/util/perl/bio-tab2rdf.pl
branches/stripped-down-version/src/util/perl/cleanupdata.pl
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/Settings.java
branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/stripped-down-version/src/war/atlas2rdf.jsp
branches/stripped-down-version/src/war/jsp-bio2rdf/obo-xref2rdf.jsp
Added Paths:
-----------
branches/stripped-down-version/src/util/perl/bio-tab2rdf.pl~
branches/stripped-down-version/src/util/perl/cleanupdata.pl~
branches/stripped-down-version/src/util/perl/elmo.pl~
branches/stripped-down-version/src/util/perl/geneid2mysql.pl
branches/stripped-down-version/src/util/perl/generic-Mysql-XML2RDF.pl
branches/stripped-down-version/src/util/perl/hgnc-csv2rdf.pl~
branches/stripped-down-version/src/util/perl/homologene2rdf.pl
branches/stripped-down-version/src/util/perl/loadvirtuoso.pl~
branches/stripped-down-version/src/util/perl/mysql2sesame.pl~
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branches/stripped-down-version/src/util/perl/regulondb-tab2rdf.pl~
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branches/stripped-down-version/src/util/shell/gene2xml.sh
branches/stripped-down-version/src/util/shell/geneid-wget.sh
branches/stripped-down-version/src/util/shell/load_ttl.sh~
branches/stripped-down-version/src/war/jsp-bio2rdf/bio2rdf-demo.rdf~
branches/stripped-down-version/src/war/jsp-bio2rdf/bio2rdf-header2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/biocarta-all-http2rdf.jsp
branches/stripped-down-version/src/war/jsp-bio2rdf/biocarta-category-http2rdf.jsp
branches/stripped-down-version/src/war/jsp-bio2rdf/biocarta-pathway-http2rdf.jsp
branches/stripped-down-version/src/war/jsp-bio2rdf/biopax-xref2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/biopax2bpl-v1.jsp~
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branches/stripped-down-version/src/war/jsp-bio2rdf/kegg-search-http2rdf.jsp~
branches/stripped-down-version/src/war/jsp-bio2rdf/lsid-bio2rdf2lsid.jsp~
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branches/stripped-down-version/src/war/robots.txt
branches/stripped-down-version/src/war/sitemap.xml
branches/stripped-down-version/src/war/xsl-sources/
branches/stripped-down-version/src/war/xsl-sources/geneid.xsl
branches/stripped-down-version/src/war/xsl-sources/obo.xsl
branches/stripped-down-version/src/war/xsl-sources/pubmed.xsl
Property Changed:
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branches/stripped-down-version/
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From: <p_a...@us...> - 2008-08-21 11:01:17
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Revision: 93
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=93&view=rev
Author: p_ansell
Date: 2008-08-21 11:01:26 +0000 (Thu, 21 Aug 2008)
Log Message:
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more additions, including index and html abilities, and some changes to the tab2rdf script, it is currently broken I think
Modified Paths:
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branches/stripped-down-version/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
branches/stripped-down-version/src/war/WEB-INF/urlrewrite.xml
branches/stripped-down-version/src/war/atlas2rdf.jsp
Added Paths:
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branches/stripped-down-version/src/util/perl/bio-tab2rdf.pl
Removed Paths:
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branches/stripped-down-version/src/util/perl/regulondb-tab2rdf.pl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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