bio2rdf-svncommits

[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[126] trunk/src

[<p_a...@us...>]

Revision: 126
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=126&view=rev
Author:   p_ansell
Date:     2008-10-16 03:58:05 +0000 (Thu, 16 Oct 2008)

Log Message:
-----------
update headers and README

Modified Paths:
--------------
    trunk/src/util/perl/cleanupdata.pl
    trunk/src/war/README
    trunk/src/war/atlas2rdf.jsp
    trunk/src/war/jsp-bio2rdf/construct-synonyme2rdf.jsp
    trunk/src/war/jsp-bio2rdf/gdb-http2bio2rdf.jsp
    trunk/src/war/jsp-bio2rdf/go-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/hugo-http2bio2rdf.jsp
    trunk/src/war/jsp-bio2rdf/kegg-search-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/lsid-bio2rdf2lsid.jsp
    trunk/src/war/jsp-bio2rdf/lsid-sameas2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-genbank2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-geneid2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-map-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-mesh-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-omim2rdf.jsp
    trunk/src/war/jsp-bio2rdf/ncbi-pubmed2rdf.jsp
    trunk/src/war/jsp-bio2rdf/pdb-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/reactome-taxon-all-http2seealso.jsp
    trunk/src/war/jsp-bio2rdf/reactome-taxon-http2seealso.jsp
    trunk/src/war/jsp-bio2rdf/search-rdfdata.jsp
    trunk/src/war/jsp-bio2rdf/search-v1.jsp
    trunk/src/war/jsp-bio2rdf/search.jsp
    trunk/src/war/jsp-bio2rdf/swoogle-search2rdf.jsp
    trunk/src/war/jsp-bio2rdf/uniprot-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/uniprot-keyword-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/uniprot-search-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/wsdl-authority.jsp
    trunk/src/war/jsp-bio2rdf/wsdl-service.jsp
    trunk/src/war/jsp-bio2rdf/wsdl-service2rdf.jsp
    trunk/src/war/xsl-sources/pubmed.xsl


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[152] trunk/src

[<p_a...@us...>]

Revision: 152
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=152&view=rev
Author:   p_ansell
Date:     2008-11-02 23:34:58 +0000 (Sun, 02 Nov 2008)

Log Message:
-----------
add debug page, and the rsync script for backing up the sourceforge svn repository

Modified Paths:
--------------
    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/bio2rdf.properties
    trunk/src/war/WEB-INF/urlrewrite.xml

Added Paths:
-----------
    trunk/src/util/shell/backupbio2rdfrsync.sh
    trunk/src/war/debug-configuration.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[157] trunk/src

[<p_a...@us...>]

Revision: 157
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=157&view=rev
Author:   p_ansell
Date:     2008-11-11 10:06:33 +0000 (Tue, 11 Nov 2008)

Log Message:
-----------
add new pieces to support namespacecounts and other statistics based queries

Modified Paths:
--------------
    trunk/src/util/perl/bio-tab2rdf.pl
    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/SparqlQueryCreator.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlRdfFetchController.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/WEB-INF/urlrewrite.xml
    trunk/src/war/atlas2rdf.jsp
    trunk/src/war/demo.rdf
    trunk/src/war/includes-css/bio2rdf.css

Added Paths:
-----------
    trunk/src/war/biopax.owl
    trunk/src/war/jsp-bio2rdf/namespacecounts.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[161] trunk/src

[<p_a...@us...>]

Revision: 161
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=161&view=rev
Author:   p_ansell
Date:     2008-11-17 06:33:10 +0000 (Mon, 17 Nov 2008)

Log Message:
-----------
fix up searchns and add prosite biopatml2rdf converter

Modified Paths:
--------------
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/WEB-INF/urlrewrite.xml

Added Paths:
-----------
    trunk/src/util/perl/flybase-rdf2rdf.pl
    trunk/src/util/perl/prosite-biopatml2rdf.pl


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[162] trunk/src

[<p_a...@us...>]

Revision: 162
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=162&view=rev
Author:   p_ansell
Date:     2008-11-18 02:03:38 +0000 (Tue, 18 Nov 2008)

Log Message:
-----------
fix url encoding so that it always uses %20 for spaces instead of + so that everything is simple and consistent. needs to be consistent for sparql queries to work correctly as they are bit sensitive

Modified Paths:
--------------
    trunk/src/util/perl/prosite-biopatml2rdf.pl
    trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcher.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/jsp-bio2rdf/kegg-search-http2rdf.jsp
    trunk/src/war/jsp-bio2rdf/swoogle-search2rdf.jsp
    trunk/src/war/jsp-bio2rdf/uniprot-search-http2rdf.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[170] trunk/src

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Revision: 170
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=170&view=rev
Author:   p_ansell
Date:     2008-11-25 02:18:49 +0000 (Tue, 25 Nov 2008)

Log Message:
-----------
changes to support the use of different protocols other than sparql to use for getting data, and commit unworking jsp script for sindice search

Modified Paths:
--------------
    trunk/src/util/perl/cleanupdata.pl
    trunk/src/war/WEB-INF/src/log4j.properties
    trunk/src/war/WEB-INF/src/org/bio2rdf/BlacklistController.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcherSparqlQueryRunnable.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
    trunk/src/war/bio2rdf.owl
    trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
    trunk/src/war/jsp-bio2rdf/swoogle-search2rdf.jsp
    trunk/src/war/redirectToId.jsp

Added Paths:
-----------
    trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcherQueryRunnable.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetcherUriQueryRunnable.java
    trunk/src/war/jsp-bio2rdf/sindice-search2rdf.jsp

Removed Paths:
-------------
    trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlRdfFetchController.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[176] trunk/src

[<p_a...@us...>]

Revision: 176
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=176&view=rev
Author:   p_ansell
Date:     2008-11-26 02:42:26 +0000 (Wed, 26 Nov 2008)

Log Message:
-----------
fix prosite-biopatml rdf:type value and add in the bug number for the sesame bug

Modified Paths:
--------------
    trunk/src/util/perl/prosite-biopatml2rdf.pl
    trunk/src/war/error-sesame-output.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[195] trunk/src

[<p_a...@us...>]

Revision: 195
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=195&view=rev
Author:   p_ansell
Date:     2009-03-01 23:26:38 +0000 (Sun, 01 Mar 2009)

Log Message:
-----------
more updates, including pubmed stylesheet and regulondb transformations to rdf

Modified Paths:
--------------
    trunk/src/util/perl/bio-tab2rdf.pl
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/xsl-sources/pubchem.xsl


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[215] trunk/src

[<p_a...@us...>]

Revision: 215
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=215&view=rev
Author:   p_ansell
Date:     2009-03-16 06:12:00 +0000 (Mon, 16 Mar 2009)

Log Message:
-----------
add some other rdfisers and modify properties file

Modified Paths:
--------------
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties

Added Paths:
-----------
    trunk/src/util/perl/go2n3.pl
    trunk/src/util/perl/mysql2n3.pl
    trunk/src/util/shell/go-wget.sh
    trunk/src/util/shell/go2mysql.sh


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[218] trunk/src

[<p_a...@us...>]

Revision: 218
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=218&view=rev
Author:   p_ansell
Date:     2009-03-18 01:19:14 +0000 (Wed, 18 Mar 2009)

Log Message:
-----------
ecocyc fix and minor changes to pipe and properties

Modified Paths:
--------------
    trunk/src/util/python/ecocyc-load-commands.txt
    trunk/src/util/python/ecocyc-proteinfeatures2rdf.py
    trunk/src/war/WEB-INF/src/constructbio2rdf.pipe
    trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/error-sesame-output.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[341] trunk/src

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Revision: 341
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=341&view=rev
Author:   p_ansell
Date:     2009-04-21 05:59:19 +0000 (Tue, 21 Apr 2009)

Log Message:
-----------
add rdfisers from wiki

Modified Paths:
--------------
    trunk/src/util/sql/create_virtuoso_index.sql
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties

Added Paths:
-----------
    trunk/src/util/perl/affymetrix-http2files.pl
    trunk/src/util/perl/affymetrix2n3.pl
    trunk/src/util/perl/cpath2mysql.pl
    trunk/src/util/perl/homologene2n3.pl
    trunk/src/util/perl/iproclass2n3.pl
    trunk/src/util/perl/n32n3.pl
    trunk/src/util/perl/namespace2rdf.pl
    trunk/src/util/perl/obo-type2n3.pl
    trunk/src/util/perl/unists2n3.pl
    trunk/src/util/perl/uri2tab.pl
    trunk/src/util/shell/count-ns.sh
    trunk/src/util/shell/hgnc-wget.sh
    trunk/src/util/shell/homologene-wget.sh
    trunk/src/util/shell/pir-wget.sh
    trunk/src/util/shell/unists-wget.sh
    trunk/src/util/sparql/
    trunk/src/util/sparql/biopax-db.sparql
    trunk/src/util/sparql/biopax2xref.sparql
    trunk/src/util/sparql/obo-uri.sparql
    trunk/src/util/sql/count-ns.sql
    trunk/src/util/sql/create-triples.sql


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[346] trunk/src

[<p_a...@us...>]

Revision: 346
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=346&view=rev
Author:   p_ansell
Date:     2009-04-23 05:15:18 +0000 (Thu, 23 Apr 2009)

Log Message:
-----------
more properties and add first sideeffects rdfiser

Modified Paths:
--------------
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties

Added Paths:
-----------
    trunk/src/util/python/sideeffects-labels2rdf.py


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[356] trunk/src

[<p_a...@us...>]

Revision: 356
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=356&view=rev
Author:   p_ansell
Date:     2009-04-26 07:19:10 +0000 (Sun, 26 Apr 2009)

Log Message:
-----------
add more instructions and rewrites to fix common mistakes and link to demo from index.html for random crawlers to have a place to start from as per design for human users also

Modified Paths:
--------------
    trunk/src/util/shell/sed_fix_go_association.sh
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
    trunk/src/war/WEB-INF/urlrewrite.xml
    trunk/src/war/mquter-index.html
    trunk/src/war/quebec-index.html


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[495] trunk/src

[<p_a...@us...>]

Revision: 495
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=495&view=rev
Author:   p_ansell
Date:     2009-05-28 22:37:15 +0000 (Thu, 28 May 2009)

Log Message:
-----------
add some more changes including a myexp_contenttype rule and namespace that was missing so far

Modified Paths:
--------------
    trunk/src/util/python/sideeffects-labels2rdf.py
    trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[557] trunk/src

[<p_a...@us...>]

Revision: 557
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=557&view=rev
Author:   p_ansell
Date:     2009-06-22 02:28:45 +0000 (Mon, 22 Jun 2009)

Log Message:
-----------
commit changes to the standard URI for the other related files

Modified Paths:
--------------
    trunk/src/util/perl/affymetrix2n3.pl
    trunk/src/util/perl/bio-tab2rdf.pl
    trunk/src/util/perl/elmo.pl
    trunk/src/util/perl/flybase-rdf2rdf.pl
    trunk/src/util/perl/freebase2n3.pl
    trunk/src/util/perl/go2n3.pl
    trunk/src/util/perl/hgnc-csv2rdf.pl
    trunk/src/util/perl/homologene2n3.pl
    trunk/src/util/perl/homologene2rdf.pl
    trunk/src/util/perl/iproclass2n3.pl
    trunk/src/util/perl/ligand-file2rdf.pl
    trunk/src/util/perl/mgi2n3.pl
    trunk/src/util/perl/mysql2sesame.pl
    trunk/src/util/perl/namespace2rdf.pl
    trunk/src/util/perl/obo-type2n3.pl
    trunk/src/util/perl/prosite-biopatml2rdf.pl
    trunk/src/util/perl/regulondb-virtuoso.pl
    trunk/src/util/perl/unists2n3.pl
    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-load-commands.txt
    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/util/python/sideeffects-adverseeffects2rdf.py
    trunk/src/util/python/sideeffects-labels2rdf.py
    trunk/src/util/sparql/biopax-db.sparql
    trunk/src/util/sparql/biopax2xref.sparql
    trunk/src/util/sparql/obo-uri.sparql
    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-ruletests-config.n3
    trunk/src/war/WEB-INF/src/bio2rdf_basic_from_uri.pipe
    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
    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_ncbigi.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
    trunk/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml_linkstonamespace_style.pipe
    trunk/src/war/WEB-INF/src/bio2rdf_uri_rank.pipe
    trunk/src/war/WEB-INF/src/bio2rdf_uri_rank_from_uri.pipe
    trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
    trunk/src/war/bio2rdf.owl
    trunk/src/war/bio2rdfpipes.jsp
    trunk/src/war/biopatml.owl
    trunk/src/war/biopax.owl
    trunk/src/war/demo.rdf
    trunk/src/war/sitemap.xml
    trunk/src/war/xsl-sources/bind.xsl
    trunk/src/war/xsl-sources/biopatml.xsl
    trunk/src/war/xsl-sources/geneid.xsl
    trunk/src/war/xsl-sources/pubchem.xsl
    trunk/src/war/xsl-sources/pubmed.xsl


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[850] trunk/src

[<p_a...@us...>]

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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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[934] trunk/src

[<p_a...@us...>]

Revision: 934
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=934&view=rev
Author:   p_ansell
Date:     2011-02-06 01:30:28 +0000 (Sun, 06 Feb 2011)

Log Message:
-----------
move pipes back to war from the jar file

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/webapp-config-bio2rdf-default.n3

Added Paths:
-----------
    trunk/src/war/WEB-INF/pipes/
    trunk/src/war/WEB-INF/pipes/bio2rdf_all_partial_common_uris.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_basic.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_basic_from_multiple_uri.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_basic_from_uri.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_pr_tr_co_in_bi_ci_mesh.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_promoter_transcriptionunits.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_promoter_transcriptionunits_components.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites_citations.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_regulators.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_regulators_citations.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ecocyc_regulators_citations_short.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_symbol.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_to_drugbank.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_to_drugbank_drugs.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_to_drugbank_targets.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_to_uniprot.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_geneid_to_hgnc_to_uniprot_to_drugbank.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_gi_geneid_iproclass.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_gi_to_geneid_to_pubmed.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_gi_to_go.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_gi_to_pubmed.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_linkstonamespace_from_multiple_helper.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_multiple_by_namespace.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ncbigi_to_pubmed_to_mesh.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_ncbigi_to_pubmed_to_mesh_labels.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_partial_common_uris_by_namespace.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_similar_drugbank_drugs_by_drugbank_targets.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_similar_drugbank_targets_by_pfam_pdb.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_subject_object_slicing.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_subject_object_slicing_from_uri.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_transform_uri_rdfxml.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_transform_uri_rdfxml_linksns_style.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_transform_uri_rdfxml_linkstonamespace_style.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_uri_rank.pipe
    trunk/src/war/WEB-INF/pipes/bio2rdf_uri_rank_from_uri.pipe
    trunk/src/war/WEB-INF/pipes/cache.ccf
    trunk/src/war/WEB-INF/pipes/operatormapping.xml
    trunk/src/war/WEB-INF/pipes/pipes.list

Removed Paths:
-------------
    trunk/src/jar/src/bio2rdf_all_partial_common_uris.pipe
    trunk/src/jar/src/bio2rdf_basic.pipe
    trunk/src/jar/src/bio2rdf_basic_from_multiple_uri.pipe
    trunk/src/jar/src/bio2rdf_basic_from_uri.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_pr_tr_co_in_bi_ci_mesh.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_promoter_transcriptionunits.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_promoter_transcriptionunits_components.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_promoter_transcriptionunits_components_involvedinregulations_bindingsites_citations.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_regulators.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_regulators_citations.pipe
    trunk/src/jar/src/bio2rdf_ecocyc_regulators_citations_short.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_symbol.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_to_drugbank.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_to_drugbank_drugs.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_to_drugbank_targets.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_to_uniprot.pipe
    trunk/src/jar/src/bio2rdf_geneid_to_hgnc_to_uniprot_to_drugbank.pipe
    trunk/src/jar/src/bio2rdf_gi_geneid_iproclass.pipe
    trunk/src/jar/src/bio2rdf_gi_to_geneid_to_pubmed.pipe
    trunk/src/jar/src/bio2rdf_gi_to_go.pipe
    trunk/src/jar/src/bio2rdf_gi_to_pubmed.pipe
    trunk/src/jar/src/bio2rdf_linkstonamespace_from_multiple_helper.pipe
    trunk/src/jar/src/bio2rdf_multiple_by_namespace.pipe
    trunk/src/jar/src/bio2rdf_ncbigi_to_pubmed_to_mesh.pipe
    trunk/src/jar/src/bio2rdf_ncbigi_to_pubmed_to_mesh_labels.pipe
    trunk/src/jar/src/bio2rdf_partial_common_uris_by_namespace.pipe
    trunk/src/jar/src/bio2rdf_similar_drugbank_drugs_by_drugbank_targets.pipe
    trunk/src/jar/src/bio2rdf_similar_drugbank_targets_by_pfam_pdb.pipe
    trunk/src/jar/src/bio2rdf_subject_object_slicing.pipe
    trunk/src/jar/src/bio2rdf_subject_object_slicing_from_uri.pipe
    trunk/src/jar/src/bio2rdf_transform_uri_rdfxml.pipe
    trunk/src/jar/src/bio2rdf_transform_uri_rdfxml_linksns_style.pipe
    trunk/src/jar/src/bio2rdf_transform_uri_rdfxml_linkstonamespace_style.pipe
    trunk/src/jar/src/bio2rdf_uri_rank.pipe
    trunk/src/jar/src/bio2rdf_uri_rank_from_uri.pipe
    trunk/src/jar/src/cache.ccf
    trunk/src/jar/src/operatormapping.xml
    trunk/src/jar/src/pipes.list


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[937] trunk/src

[<p_a...@us...>]

Revision: 937
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=937&view=rev
Author:   p_ansell
Date:     2011-02-06 07:30:25 +0000 (Sun, 06 Feb 2011)

Log Message:
-----------
extensive refactoring, not complete yet

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/NamespaceEntry.java
    trunk/src/api-jar/src/org/queryall/Provider.java
    trunk/src/api-jar/src/org/queryall/QueryType.java
    trunk/src/jar/src/org/queryall/blacklist/BlacklistController.java
    trunk/src/jar/src/org/queryall/blacklist/BlacklistEntry.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/helpers/SparqlQueryCreator.java
    trunk/src/jar/src/org/queryall/helpers/Utilities.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/ProfileImpl.java
    trunk/src/jar/src/org/queryall/impl/ProjectImpl.java
    trunk/src/jar/src/org/queryall/impl/ProviderImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java
    trunk/src/jar/src/org/queryall/impl/RegexNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/RuleTestImpl.java
    trunk/src/jar/src/org/queryall/impl/SparqlNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/TemplateImpl.java
    trunk/src/jar/src/org/queryall/queryutils/HttpUrlQueryRunnable.java
    trunk/src/jar/src/org/queryall/queryutils/ProvenanceRecord.java
    trunk/src/jar/src/org/queryall/queryutils/QueryBundle.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetchController.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcher.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherSparqlQueryRunnable.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherUriQueryRunnable.java
    trunk/src/jar/src/org/queryall/servlets/GeneralServlet.java
    trunk/src/jar/src/org/queryall/servlets/ProfilesServlet.java
    trunk/src/jar/src/org/queryall/servlets/QueryAllSchemaServlet.java
    trunk/src/jar/src/org/queryall/servlets/RobotsTxtServlet.java
    trunk/src/jar/src/org/queryall/servlets/html/HtmlPageRenderer.java
    trunk/src/jar/src/org/queryall/servlets/queryparsers/ConfigurationQueryOptions.java
    trunk/src/jar/src/org/queryall/servlets/queryparsers/DefaultQueryOptions.java
    trunk/src/jar/src/org/queryall/servlets/queryparsers/RuleTesterQueryOptions.java
    trunk/src/jar/src/org/queryall/statistics/StatisticsEntry.java
    trunk/src/war/WEB-INF/classes/log4j.properties
    trunk/src/war/WEB-INF/templates/endpoints.vm
    trunk/src/war/WEB-INF/web-production-template.xml
    trunk/src/war/blacklisterror.jsp
    trunk/src/war/jsp-bio2rdf/crossref-openurldoi2rdf.jsp
    trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
    trunk/src/war/multifetch.jsp

Added Paths:
-----------
    trunk/src/api-jar/src/org/queryall/Template.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[938] trunk/src

[<p_a...@us...>]

Revision: 938
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=938&view=rev
Author:   p_ansell
Date:     2011-02-06 07:58:02 +0000 (Sun, 06 Feb 2011)

Log Message:
-----------
more refactoring, still not complete

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/api-jar/src/org/queryall/QueryType.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[939] trunk/src

[<p_a...@us...>]

Revision: 939
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=939&view=rev
Author:   p_ansell
Date:     2011-02-07 04:30:48 +0000 (Mon, 07 Feb 2011)

Log Message:
-----------
more refactoring

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/api-jar/src/org/queryall/Profile.java
    trunk/src/api-jar/src/org/queryall/Provider.java
    trunk/src/api-jar/src/org/queryall/QueryType.java
    trunk/src/api-jar/src/org/queryall/RuleTest.java
    trunk/src/api-jar/src/org/queryall/Template.java
    trunk/src/jar/src/org/queryall/blacklist/BlacklistEntry.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/helpers/SparqlQueryCreator.java
    trunk/src/jar/src/org/queryall/helpers/Utilities.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/ProfileImpl.java
    trunk/src/jar/src/org/queryall/impl/ProjectImpl.java
    trunk/src/jar/src/org/queryall/impl/ProviderImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java
    trunk/src/jar/src/org/queryall/impl/RegexNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/RuleTestImpl.java
    trunk/src/jar/src/org/queryall/impl/SparqlNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/TemplateImpl.java
    trunk/src/jar/src/org/queryall/queryutils/ProvenanceRecord.java
    trunk/src/jar/src/org/queryall/queryutils/QueryBundle.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetchController.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherSparqlQueryRunnable.java
    trunk/src/jar/src/org/queryall/servlets/ProfilesServlet.java
    trunk/src/jar/src/org/queryall/servlets/QueryAllSchemaServlet.java
    trunk/src/war/namespaceproviders.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[940] trunk/src

[<p_a...@us...>]

Revision: 940
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=940&view=rev
Author:   p_ansell
Date:     2011-02-08 04:11:58 +0000 (Tue, 08 Feb 2011)

Log Message:
-----------
more refactoring

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/BaseQueryAllInterface.java
    trunk/src/api-jar/src/org/queryall/NamespaceEntry.java
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/api-jar/src/org/queryall/Provider.java
    trunk/src/api-jar/src/org/queryall/QueryType.java
    trunk/src/api-jar/src/org/queryall/RuleTest.java
    trunk/src/jar/src/org/queryall/helpers/Utilities.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/ProfileImpl.java
    trunk/src/jar/src/org/queryall/impl/ProjectImpl.java
    trunk/src/jar/src/org/queryall/impl/ProviderImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java
    trunk/src/jar/src/org/queryall/impl/RegexNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/RuleTestImpl.java
    trunk/src/jar/src/org/queryall/impl/SparqlNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/TemplateImpl.java
    trunk/src/jar/src/org/queryall/queryutils/ProvenanceRecord.java
    trunk/src/jar/src/org/queryall/queryutils/QueryBundle.java
    trunk/src/jar/src/org/queryall/statistics/StatisticsEntry.java
    trunk/src/war/multifetch.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[941] trunk/src

[<p_a...@us...>]

Revision: 941
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=941&view=rev
Author:   p_ansell
Date:     2011-02-08 04:36:27 +0000 (Tue, 08 Feb 2011)

Log Message:
-----------
change key to be URI in all locations in the base interface, breaking quite a number of places more than already broken

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/BaseQueryAllInterface.java
    trunk/src/api-jar/src/org/queryall/Profile.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/impl/ProfileImpl.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[942] trunk/src

[<p_a...@us...>]

Revision: 942
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=942&view=rev
Author:   p_ansell
Date:     2011-02-08 04:43:44 +0000 (Tue, 08 Feb 2011)

Log Message:
-----------
change toRdf method to use URI as well, breaking more things

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/BaseQueryAllInterface.java
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/jar/src/org/queryall/blacklist/BlacklistEntry.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/helpers/SparqlQueryCreator.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[943] trunk/src

[<p_a...@us...>]

Revision: 943
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=943&view=rev
Author:   p_ansell
Date:     2011-02-08 07:47:13 +0000 (Tue, 08 Feb 2011)

Log Message:
-----------
most of the way through refactoring, still quite a few changes to go though

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/Profile.java
    trunk/src/api-jar/src/org/queryall/Provider.java
    trunk/src/api-jar/src/org/queryall/Template.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/helpers/SparqlQueryCreator.java
    trunk/src/jar/src/org/queryall/helpers/Utilities.java
    trunk/src/jar/src/org/queryall/impl/NamespaceEntryImpl.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/ProfileImpl.java
    trunk/src/jar/src/org/queryall/impl/ProjectImpl.java
    trunk/src/jar/src/org/queryall/impl/ProviderImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java
    trunk/src/jar/src/org/queryall/impl/RegexNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/RuleTestImpl.java
    trunk/src/jar/src/org/queryall/impl/SparqlNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/TemplateImpl.java
    trunk/src/jar/src/org/queryall/queryutils/ProvenanceRecord.java
    trunk/src/jar/src/org/queryall/queryutils/QueryBundle.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetchController.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcher.java
    trunk/src/jar/src/org/queryall/servlets/ConfigurationServlet.java
    trunk/src/jar/src/org/queryall/servlets/GeneralServlet.java
    trunk/src/jar/src/org/queryall/servlets/ProfilesServlet.java
    trunk/src/jar/src/org/queryall/servlets/QueryAllSchemaServlet.java
    trunk/src/jar/src/org/queryall/servlets/QueryallContentNegotiator.java
    trunk/src/jar/src/org/queryall/servlets/RuleTesterServlet.java
    trunk/src/jar/src/org/queryall/statistics/StatisticsEntry.java
    trunk/src/war/WEB-INF/templates/endpoints.vm


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[944] trunk/src

[<p_a...@us...>]

Revision: 944
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=944&view=rev
Author:   p_ansell
Date:     2011-02-08 10:23:08 +0000 (Tue, 08 Feb 2011)

Log Message:
-----------
more refactoring, ~20 compile time bugs left

Modified Paths:
--------------
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/api-jar/src/org/queryall/Provider.java
    trunk/src/api-jar/src/org/queryall/QueryType.java
    trunk/src/jar/src/org/queryall/blacklist/BlacklistController.java
    trunk/src/jar/src/org/queryall/helpers/Settings.java
    trunk/src/jar/src/org/queryall/helpers/SparqlQueryCreator.java
    trunk/src/jar/src/org/queryall/helpers/Utilities.java
    trunk/src/jar/src/org/queryall/impl/NormalisationRuleImpl.java
    trunk/src/jar/src/org/queryall/impl/ProviderImpl.java
    trunk/src/jar/src/org/queryall/impl/QueryTypeImpl.java
    trunk/src/jar/src/org/queryall/impl/RegexNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/RuleTestImpl.java
    trunk/src/jar/src/org/queryall/impl/SparqlNormalisationRule.java
    trunk/src/jar/src/org/queryall/impl/TemplateImpl.java
    trunk/src/jar/src/org/queryall/queryutils/QueryDebug.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetchController.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherQueryRunnable.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherSparqlQueryRunnable.java
    trunk/src/jar/src/org/queryall/queryutils/RdfFetcherUriQueryRunnable.java
    trunk/src/jar/src/org/queryall/servlets/ConfigurationServlet.java
    trunk/src/jar/src/org/queryall/servlets/GeneralServlet.java
    trunk/src/jar/src/org/queryall/servlets/ManualRefreshServlet.java
    trunk/src/jar/src/org/queryall/servlets/RuleTesterServlet.java
    trunk/src/jar/src/org/queryall/servlets/html/HtmlPageRenderer.java
    trunk/src/jar/src/org/queryall/servlets/html/VelocityHelper.java


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