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

From: <p_a...@us...> - 2011-02-08 04:43:50

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:[941] trunk/src

From: <p_a...@us...> - 2011-02-08 04:36:33

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:[940] trunk/src

From: <p_a...@us...> - 2011-02-08 04:12:05

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:[939] trunk/src

From: <p_a...@us...> - 2011-02-07 04:30:55

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:[938] trunk/src

From: <p_a...@us...> - 2011-02-06 07:58:09

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:[937] trunk/src

From: <p_a...@us...> - 2011-02-06 07:30:31

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:[936] trunk

From: <p_a...@us...> - 2011-02-06 05:34:29

Revision: 936
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=936&view=rev
Author:   p_ansell
Date:     2011-02-06 05:34:23 +0000 (Sun, 06 Feb 2011)

Log Message:
-----------
move a large number of things around in the heirarchy and create interfaces for each of the main model objects

Modified Paths:
--------------
    trunk/build.xml
    trunk/src/api-jar/src/org/queryall/BaseQueryAllInterface.java
    trunk/src/api-jar/src/org/queryall/NormalisationRule.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/war/WEB-INF/autogenerated-bio2rdf-query-insert-providers-config.n3
    trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
    trunk/src/war/WEB-INF/classes/log4j.properties
    trunk/src/war/WEB-INF/sharednames-configuration.n3
    trunk/src/war/WEB-INF/test-configuration.n3
    trunk/src/war/bio2rdfpipes.jsp
    trunk/src/war/blacklisterror.jsp
    trunk/src/war/jsp-bio2rdf/namespacecounts.jsp
    trunk/src/war/multifetch.jsp
    trunk/src/war/namespaceproviders.jsp

Added Paths:
-----------
    trunk/src/api-jar/src/org/queryall/NamespaceEntry.java
    trunk/src/api-jar/src/org/queryall/Profile.java
    trunk/src/api-jar/src/org/queryall/Project.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/blacklist/
    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/
    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/helpers/VoidUtility.java
    trunk/src/jar/src/org/queryall/impl/
    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/
    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/QueryDebug.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/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/QueryallContentNegotiator.java
    trunk/src/jar/src/org/queryall/servlets/QueryallLanguageNegotiator.java
    trunk/src/jar/src/org/queryall/servlets/html/
    trunk/src/jar/src/org/queryall/servlets/html/HtmlPageRenderer.java
    trunk/src/jar/src/org/queryall/servlets/html/VelocityHelper.java
    trunk/src/jar/src/org/queryall/statistics/
    trunk/src/jar/src/org/queryall/statistics/StatisticsEntry.java

Removed Paths:
-------------
    trunk/src/jar/src/org/bio2rdf/


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[935] trunk

From: <p_a...@us...> - 2011-02-06 03:32:45

Revision: 935
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=935&view=rev
Author:   p_ansell
Date:     2011-02-06 03:32:38 +0000 (Sun, 06 Feb 2011)

Log Message:
-----------
rearrange a large number of things, and add in a new api jar file build to make it easy to have alternate implementations of the interface in future since things are being rearranged now anyway

Modified Paths:
--------------
    trunk/build.xml
    trunk/src/war/WEB-INF/autogenerated-bio2rdf-query-insert-providers-config.n3
    trunk/src/war/WEB-INF/base-bio2rdf-providers-html-config.n3
    trunk/src/war/WEB-INF/carleton-configuration.n3
    trunk/src/war/WEB-INF/sharednames-configuration.n3
    trunk/src/war/WEB-INF/urlrewrite.xml
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-carleton.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-default.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-mquter.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-quebec.n3
    trunk/src/war/WEB-INF/webapp-config-default-carleton-bio2rdf-template.n3
    trunk/src/war/WEB-INF/webapp-config-default-mquter-bio2rdf-template.n3
    trunk/src/war/WEB-INF/webapp-config-default-quebec-bio2rdf-template.n3

Added Paths:
-----------
    trunk/src/api-jar/
    trunk/src/api-jar/src/
    trunk/src/api-jar/src/org/
    trunk/src/api-jar/src/org/queryall/
    trunk/src/api-jar/src/org/queryall/BaseQueryAllInterface.java
    trunk/src/api-jar/src/org/queryall/NormalisationRule.java
    trunk/src/jar/src/org/queryall/servlets/
    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/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/RuleTesterServlet.java
    trunk/src/jar/src/org/queryall/servlets/queryparsers/
    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

Removed Paths:
-------------
    trunk/src/jar/src/org/queryall/ConfigurationQueryOptions.java
    trunk/src/jar/src/org/queryall/ConfigurationServlet.java
    trunk/src/jar/src/org/queryall/DefaultQueryOptions.java
    trunk/src/jar/src/org/queryall/GeneralServlet.java
    trunk/src/jar/src/org/queryall/ManualRefreshServlet.java
    trunk/src/jar/src/org/queryall/NormalisationRule.java
    trunk/src/jar/src/org/queryall/ProfilesServlet.java
    trunk/src/jar/src/org/queryall/QueryAllSchemaServlet.java
    trunk/src/jar/src/org/queryall/RdfCompatible.java
    trunk/src/jar/src/org/queryall/RobotsTxtServlet.java
    trunk/src/jar/src/org/queryall/RuleTesterQueryOptions.java
    trunk/src/jar/src/org/queryall/RuleTesterServlet.java

Property Changed:
----------------
    trunk/src/war/WEB-INF/autogenerated-bio2rdf-query-insert-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/basicrdffile.n3
    trunk/src/war/WEB-INF/carleton-configuration.n3
    trunk/src/war/WEB-INF/my-local-configuration-example.n3
    trunk/src/war/WEB-INF/sharednames-configuration.n3
    trunk/src/war/WEB-INF/test-configuration.n3
    trunk/src/war/WEB-INF/test-simplest-configuration.n3
    trunk/src/war/WEB-INF/void-example.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-carleton.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-default.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-mquter.n3
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-quebec.n3
    trunk/src/war/WEB-INF/webapp-config-default-carleton-bio2rdf-template.n3
    trunk/src/war/WEB-INF/webapp-config-default-mquter-bio2rdf-template.n3
    trunk/src/war/WEB-INF/webapp-config-default-quebec-bio2rdf-template.n3


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

From: <p_a...@us...> - 2011-02-06 01:30:35

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:[933] trunk/src/jar/src/org/bio2rdf/HtmlPageRenderer. java

From: <p_a...@us...> - 2011-02-04 10:52:38

Revision: 933
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=933&view=rev
Author:   p_ansell
Date:     2011-02-04 10:52:32 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
fix title generation

Modified Paths:
--------------
    trunk/src/jar/src/org/bio2rdf/HtmlPageRenderer.java


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[932] trunk/build.xml

From: <p_a...@us...> - 2011-02-04 10:30:05

Revision: 932
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=932&view=rev
Author:   p_ansell
Date:     2011-02-04 10:29:59 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
fix minor bug in build.xml

Modified Paths:
--------------
    trunk/build.xml


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[931] trunk

From: <p_a...@us...> - 2011-02-04 09:48:48

Revision: 931
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=931&view=rev
Author:   p_ansell
Date:     2011-02-04 09:48:42 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
move queryall.properties file

Modified Paths:
--------------
    trunk/build.xml
    trunk/src/jar/src/org/bio2rdf/Settings.java

Added Paths:
-----------
    trunk/src/jar/src/org/queryall/queryall.properties

Removed Paths:
-------------
    trunk/src/jar/src/org/bio2rdf/queryall.properties


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[930] trunk

From: <p_a...@us...> - 2011-02-04 08:55:49

Revision: 930
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=930&view=rev
Author:   p_ansell
Date:     2011-02-04 08:55:43 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
put log4j.properties back in its default location

Modified Paths:
--------------
    trunk/build.xml

Added Paths:
-----------
    trunk/src/war/WEB-INF/classes/
    trunk/src/war/WEB-INF/classes/log4j.properties

Removed Paths:
-------------
    trunk/src/jar/src/log4j.properties


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[929] trunk

From: <p_a...@us...> - 2011-02-04 08:36:48

Revision: 929
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=929&view=rev
Author:   p_ansell
Date:     2011-02-04 08:36:42 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
make it possible to use a jar independent of the war file

Modified Paths:
--------------
    trunk/build.xml

Added Paths:
-----------
    trunk/src/jar/
    trunk/src/jar/src/
    trunk/src/jar/src/de/fuberlin/wiwiss/pubby/negotiation/ContentTypeNegotiator.java
    trunk/src/jar/src/de/fuberlin/wiwiss/pubby/negotiation/MediaRangeSpec.java
    trunk/src/jar/src/log4j.properties
    trunk/src/jar/src/org/bio2rdf/Bio2RdfLanguageNegotiator.java
    trunk/src/jar/src/org/bio2rdf/HtmlPageRenderer.java
    trunk/src/jar/src/org/bio2rdf/ProviderConfiguration.java
    trunk/src/jar/src/org/bio2rdf/Settings.java
    trunk/src/jar/src/org/bio2rdf/StatisticsEntry.java
    trunk/src/jar/src/org/bio2rdf/Utilities.java
    trunk/src/jar/src/org/bio2rdf/queryall.properties
    trunk/src/jar/src/org/queryall/ConfigurationQueryOptions.java
    trunk/src/jar/src/org/queryall/ConfigurationServlet.java
    trunk/src/jar/src/org/queryall/DefaultQueryOptions.java
    trunk/src/jar/src/org/queryall/GeneralServlet.java
    trunk/src/jar/src/org/queryall/ManualRefreshServlet.java
    trunk/src/jar/src/org/queryall/ProfilesServlet.java
    trunk/src/jar/src/org/queryall/QueryAllSchemaServlet.java
    trunk/src/jar/src/org/queryall/RobotsTxtServlet.java
    trunk/src/jar/src/org/queryall/RuleTesterQueryOptions.java
    trunk/src/jar/src/org/queryall/RuleTesterServlet.java
    trunk/src/nonvarargs-sesamewrapper/
    trunk/src/nonvarargs-sesamewrapper/NonVarArgsRepositoryConnection.class
    trunk/src/nonvarargs-sesamewrapper/NonVarArgsRepositoryConnection.java

Removed Paths:
-------------
    trunk/src/jar/src/de/fuberlin/wiwiss/pubby/negotiation/ContentTypeNegotiator.java
    trunk/src/jar/src/de/fuberlin/wiwiss/pubby/negotiation/MediaRangeSpec.java
    trunk/src/jar/src/log4j.properties
    trunk/src/jar/src/org/bio2rdf/HtmlPageRenderer.java
    trunk/src/jar/src/org/bio2rdf/ProviderConfiguration.java
    trunk/src/jar/src/org/bio2rdf/Settings.java
    trunk/src/jar/src/org/bio2rdf/StatisticsEntry.java
    trunk/src/jar/src/org/bio2rdf/Utilities.java
    trunk/src/jar/src/org/bio2rdf/queryall.properties
    trunk/src/jar/src/org/queryall/DefaultServlet.java
    trunk/src/jar/src/org/queryall/QueryOptions.java
    trunk/src/war/META-INF/


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[928] trunk/src/war/WEB-INF

From: <p_a...@us...> - 2011-02-04 08:19:29

Revision: 928
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=928&view=rev
Author:   p_ansell
Date:     2011-02-04 08:19:23 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
remove other irrelevant directories

Removed Paths:
-------------
    trunk/src/war/WEB-INF/logs/
    trunk/src/war/WEB-INF/tmp/


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[927] trunk/src/war/WEB-INF

From: <p_a...@us...> - 2011-02-04 08:16:33

Revision: 927
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=927&view=rev
Author:   p_ansell
Date:     2011-02-04 08:16:25 +0000 (Fri, 04 Feb 2011)

Log Message:
-----------
remove irrelevant directories now

Removed Paths:
-------------
    trunk/src/war/WEB-INF/classes/
    trunk/src/war/WEB-INF/src/


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[926] trunk

From: <p_a...@us...> - 2011-02-03 03:56:00

Revision: 926
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=926&view=rev
Author:   p_ansell
Date:     2011-02-03 03:55:54 +0000 (Thu, 03 Feb 2011)

Log Message:
-----------
reform the settings so that they are initialised to start with from web.xml and not queryall.properties

Modified Paths:
--------------
    trunk/build.xml
    trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/queryall.properties
    trunk/src/war/WEB-INF/src/org/queryall/ConfigurationServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/GeneralServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/ProfilesServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/QueryAllSchemaServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/RobotsTxtServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/RuleTesterServlet.java
    trunk/src/war/WEB-INF/urlrewrite.xml
    trunk/src/war/WEB-INF/web-production-template.xml

Added Paths:
-----------
    trunk/src/war/WEB-INF/src/org/queryall/ManualRefreshServlet.java

Removed Paths:
-------------
    trunk/src/war/bio2rdf.owl
    trunk/src/war/biopatml.owl
    trunk/src/war/biopax.owl
    trunk/src/war/manualrefresh.jsp

Property Changed:
----------------
    trunk/src/war/WEB-INF/web-production-template.xml


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[925] trunk/src/war

From: <p_a...@us...> - 2011-01-28 04:13:30

Revision: 925
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=925&view=rev
Author:   p_ansell
Date:     2011-01-28 04:13:24 +0000 (Fri, 28 Jan 2011)

Log Message:
-----------
add new servlets to replace those which were previously implemented using jsp

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

Added Paths:
-----------
    trunk/src/war/WEB-INF/src/org/queryall/ConfigurationQueryOptions.java
    trunk/src/war/WEB-INF/src/org/queryall/ConfigurationServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/ProfilesServlet.java
    trunk/src/war/WEB-INF/src/org/queryall/QueryAllSchemaServlet.java

Removed Paths:
-------------
    trunk/src/war/error-sesame-output.jsp
    trunk/src/war/error-tomcat-encoded-slashes.jsp
    trunk/src/war/profiles.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[924] trunk

From: <p_a...@us...> - 2011-01-28 02:28:23

Revision: 924
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=924&view=rev
Author:   p_ansell
Date:     2011-01-28 02:28:17 +0000 (Fri, 28 Jan 2011)

Log Message:
-----------
make /queryall/ work with a servlet instead of a JSP page

Modified Paths:
--------------
    trunk/build.xml
    trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
    trunk/src/war/WEB-INF/urlrewrite.xml

Removed Paths:
-------------
    trunk/src/war/internalschema.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[923] trunk/src/war

From: <p_a...@us...> - 2011-01-28 00:44:27

Revision: 923
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=923&view=rev
Author:   p_ansell
Date:     2011-01-28 00:44:21 +0000 (Fri, 28 Jan 2011)

Log Message:
-----------
remove more jsp and static files 

Added Paths:
-----------
    trunk/src/war/WEB-INF/src/org/queryall/RobotsTxtServlet.java

Removed Paths:
-------------
    trunk/src/war/robotstxt.jsp
    trunk/src/war/scraper.rdf
    trunk/src/war/terms.owl
    trunk/src/war/test-template-use.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[922] trunk/src/war

From: <p_a...@us...> - 2011-01-28 00:20:52

Revision: 922
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=922&view=rev
Author:   p_ansell
Date:     2011-01-28 00:20:46 +0000 (Fri, 28 Jan 2011)

Log Message:
-----------
misc changes to configurations and rendering pages

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/templates/page.vm

Removed Paths:
-------------
    trunk/src/war/debug-configuration.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[921] trunk/src/war/WEB-INF/src/org/bio2rdf/Settings. java

From: <p_a...@us...> - 2010-12-11 06:30:13

Revision: 921
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=921&view=rev
Author:   p_ansell
Date:     2010-12-11 06:30:07 +0000 (Sat, 11 Dec 2010)

Log Message:
-----------
manual refresh working again

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


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[920] trunk

From: <p_a...@us...> - 2010-12-11 05:35:15

Revision: 920
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=920&view=rev
Author:   p_ansell
Date:     2010-12-11 05:35:09 +0000 (Sat, 11 Dec 2010)

Log Message:
-----------
finish making configurations work again

Modified Paths:
--------------
    trunk/build.xml
    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/Utilities.java
    trunk/src/war/WEB-INF/src/org/bio2rdf/queryall.properties
    trunk/src/war/WEB-INF/urlrewrite.xml
    trunk/src/war/WEB-INF/webapp-config-bio2rdf-default.n3


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[919] trunk/src/war

From: <p_a...@us...> - 2010-12-10 22:48:22

Revision: 919
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=919&view=rev
Author:   p_ansell
Date:     2010-12-10 22:48:12 +0000 (Fri, 10 Dec 2010)

Log Message:
-----------
remove the old jsp file for testing rules

Modified Paths:
--------------
    trunk/src/war/WEB-INF/src/log4j.properties

Removed Paths:
-------------
    trunk/src/war/test-regexmethods.jsp


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[Bio2rdf-svncommits] SF.net SVN: bio2rdf:[918] trunk/src/war/WEB-INF

From: <p_a...@us...> - 2010-12-10 22:44:10

Revision: 918
          http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=918&view=rev
Author:   p_ansell
Date:     2010-12-10 22:44:04 +0000 (Fri, 10 Dec 2010)

Log Message:
-----------
make rule tester work

Modified Paths:
--------------
    trunk/src/war/WEB-INF/base-bio2rdf-ruletests-config.n3
    trunk/src/war/WEB-INF/src/log4j.properties
    trunk/src/war/WEB-INF/src/org/queryall/RuleTesterQueryOptions.java
    trunk/src/war/WEB-INF/src/org/queryall/RuleTesterServlet.java
    trunk/src/war/WEB-INF/urlrewrite.xml


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