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From: <p_a...@us...> - 2009-03-30 07:20:14
|
Revision: 242
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=242&view=rev
Author: p_ansell
Date: 2009-03-30 07:20:09 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
tag 0.3.1 version
Modified Paths:
--------------
tags/0.3/build.xml
tags/0.3/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
Added Paths:
-----------
tags/0.3/
tags/0.3/src/util/shell/chebi-wget.sh
tags/0.3/src/util/shell/chebi2mysql.sh
tags/0.3/src/util/sql/chebi-import.sql
tags/0.3.1/
tags/0.3.1/build.xml
tags/0.3.1/src/util/shell/chebi-wget.sh
tags/0.3.1/src/util/shell/chebi2mysql.sh
tags/0.3.1/src/util/sql/chebi-import.sql
tags/0.3.1/src/war/WEB-INF/lib/pipes-0.7.1-prerelease-patched.jar
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_basic.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_basic_from_uri.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators_citations.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_ecocyc_regulators_citations_short.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_subject_object_slicing_from_uri.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_transform_uri_rdfxml_linksns_style.pipe
tags/0.3.1/src/war/WEB-INF/src/log4j.properties
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/Settings.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
tags/0.3.1/src/war/WEB-INF/src/pipes.list
tags/0.3.1/src/war/WEB-INF/urlrewrite.xml
tags/0.3.1/src/war/bio2rdfpipes.jsp
tags/0.3.1/src/war/index.html
tags/0.3.1/src/war/mquter-index.html
tags/0.3.1/src/war/namespaceproviders.jsp
tags/0.3.1/src/war/quebec-index.html
tags/0.3.1/src/war/robots.txt
tags/0.3.1/src/war/test-regexmethods.jsp
Removed Paths:
-------------
tags/0.3.1/build.xml
tags/0.3.1/src/war/WEB-INF/lib/pipes-0.7.0.jar
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_basic.pipe
tags/0.3.1/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
tags/0.3.1/src/war/WEB-INF/src/log4j.properties
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/ProviderConfiguration.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/RdfNormalisationRule.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/Settings.java
tags/0.3.1/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
tags/0.3.1/src/war/WEB-INF/src/pipes.list
tags/0.3.1/src/war/WEB-INF/urlrewrite.xml
tags/0.3.1/src/war/bio2rdfpipes.jsp
tags/0.3.1/src/war/index.html
tags/0.3.1/src/war/mquter-index.html
tags/0.3.1/src/war/quebec-index.html
tags/0.3.1/src/war/robots.txt
tags/0.3.1/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2009-03-30 07:14:04
|
Revision: 241
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=241&view=rev
Author: p_ansell
Date: 2009-03-30 07:13:59 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
make regex tests all pass if they are configured correctly, and add /admin/ to robots.txt
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/bio2rdf.properties
trunk/src/war/namespaceproviders.jsp
trunk/src/war/robots.txt
trunk/src/war/test-regexmethods.jsp
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From: <p_a...@us...> - 2009-03-30 06:02:02
|
Revision: 240
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=240&view=rev
Author: p_ansell
Date: 2009-03-30 06:01:54 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
up the logging level for PIPES to fatal as we are using some voodoo methods to get around the parameter usage restrictions that will always generate messages at the ERROR level for every pipe call, including a full stack trace
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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From: <p_a...@us...> - 2009-03-30 05:56:11
|
Revision: 239
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=239&view=rev
Author: p_ansell
Date: 2009-03-30 05:56:03 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
reduce pipes logging verbosity
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
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From: <p_a...@us...> - 2009-03-30 05:50:15
|
Revision: 238
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=238&view=rev
Author: p_ansell
Date: 2009-03-30 05:50:10 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
new pipes
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/pipes.list
Added Paths:
-----------
trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_basic_from_uri.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_subject_object_slicing.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing_from_uri.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
Removed Paths:
-------------
trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
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From: <p_a...@us...> - 2009-03-30 05:29:56
|
Revision: 237
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=237&view=rev
Author: p_ansell
Date: 2009-03-30 05:29:46 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
add Test URI's to ProviderConfigurations so that in future we can automate network analysis based on them
Modified Paths:
--------------
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
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From: <p_a...@us...> - 2009-03-30 05:03:47
|
Revision: 236
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=236&view=rev
Author: p_ansell
Date: 2009-03-30 05:03:39 +0000 (Mon, 30 Mar 2009)
Log Message:
-----------
add debugging for namespace/query/provider relationships
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/bio2rdf.properties
trunk/src/war/WEB-INF/urlrewrite.xml
Added Paths:
-----------
trunk/src/war/namespaceproviders.jsp
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From: <p_a...@us...> - 2009-03-29 03:38:07
|
Revision: 235
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=235&view=rev
Author: p_ansell
Date: 2009-03-29 03:38:03 +0000 (Sun, 29 Mar 2009)
Log Message:
-----------
new regex structure to allow for - (dashes) in namespaces and minor change to pipes.jsp
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/bio2rdfpipes.jsp
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From: <p_a...@us...> - 2009-03-29 00:45:20
|
Revision: 234
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=234&view=rev
Author: p_ansell
Date: 2009-03-29 00:45:10 +0000 (Sun, 29 Mar 2009)
Log Message:
-----------
add namespaces and fix some query types
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-27 05:05:43
|
Revision: 233
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=233&view=rev
Author: p_ansell
Date: 2009-03-27 05:05:41 +0000 (Fri, 27 Mar 2009)
Log Message:
-----------
update robots.txt and the namespace list for obo.bio2rdf.org
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/robots.txt
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From: <p_a...@us...> - 2009-03-27 01:59:59
|
Revision: 232
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=232&view=rev
Author: p_ansell
Date: 2009-03-27 01:38:07 +0000 (Fri, 27 Mar 2009)
Log Message:
-----------
add counttriples operation
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-25 23:24:23
|
Revision: 231
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=231&view=rev
Author: p_ansell
Date: 2009-03-25 23:24:18 +0000 (Wed, 25 Mar 2009)
Log Message:
-----------
add some more scripts, and edit index.html's and edit pipes and change taxonomy: to default to taxon: instead
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/index.html
trunk/src/war/mquter-index.html
trunk/src/war/quebec-index.html
Added Paths:
-----------
trunk/src/util/shell/chebi-wget.sh
trunk/src/util/shell/chebi2mysql.sh
trunk/src/util/sql/chebi-import.sql
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From: <p_a...@us...> - 2009-03-23 04:51:45
|
Revision: 230
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=230&view=rev
Author: p_ansell
Date: 2009-03-23 04:51:41 +0000 (Mon, 23 Mar 2009)
Log Message:
-----------
exchange the 0.7.0 pipes jar file for a prerelease version self-compiled with a patch to make it not use the broken sesame RDFXMLPrettyWriter
Added Paths:
-----------
trunk/src/war/WEB-INF/lib/pipes-0.7.1-prerelease-patched.jar
Removed Paths:
-------------
trunk/src/war/WEB-INF/lib/pipes-0.7.0.jar
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From: <p_a...@us...> - 2009-03-20 04:55:49
|
Revision: 229
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=229&view=rev
Author: p_ansell
Date: 2009-03-20 04:55:44 +0000 (Fri, 20 Mar 2009)
Log Message:
-----------
fix up taxonomy.bio2rdf.org/sparql rule
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-20 04:19:59
|
Revision: 228
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=228&view=rev
Author: p_ansell
Date: 2009-03-20 04:19:50 +0000 (Fri, 20 Mar 2009)
Log Message:
-----------
fix up strategy for taxon2taxonomy normalisation and sameAs
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-03-20 03:48:02
|
Revision: 227
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=227&view=rev
Author: p_ansell
Date: 2009-03-20 03:47:58 +0000 (Fri, 20 Mar 2009)
Log Message:
-----------
cleanup of atlas2rdf.jsp and start to implement nocommunication type providers in addition to httpgeturl and httppostsparql
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/RdfFetchController.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-03-20 00:10:03
|
Revision: 226
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=226&view=rev
Author: p_ansell
Date: 2009-03-20 00:09:54 +0000 (Fri, 20 Mar 2009)
Log Message:
-----------
add pipes dependencies as libraries
Added Paths:
-----------
trunk/src/war/WEB-INF/lib/saxon9-dom.jar
trunk/src/war/WEB-INF/lib/saxon9.jar
trunk/src/war/WEB-INF/lib/xpp3-1.1.4c.jar
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From: <p_a...@us...> - 2009-03-20 00:08:38
|
Revision: 225
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=225&view=rev
Author: p_ansell
Date: 2009-03-20 00:08:35 +0000 (Fri, 20 Mar 2009)
Log Message:
-----------
add dailymed and drugbank rules and provider configs and add xmlEncoded_urlEncoded_ versions of input_X and queryString for use in RDF/XML templates
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-19 01:03:27
|
Revision: 224
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=224&view=rev
Author: p_ansell
Date: 2009-03-19 01:03:16 +0000 (Thu, 19 Mar 2009)
Log Message:
-----------
update the normalisation rules for some endpoints which have recently been normalised
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-19 00:22:40
|
Revision: 223
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=223&view=rev
Author: p_ansell
Date: 2009-03-19 00:22:27 +0000 (Thu, 19 Mar 2009)
Log Message:
-----------
fix stray character
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
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From: <p_a...@us...> - 2009-03-18 23:52:32
|
Revision: 222
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=222&view=rev
Author: p_ansell
Date: 2009-03-18 23:52:27 +0000 (Wed, 18 Mar 2009)
Log Message:
-----------
make pipes work, and add hack to avoid common sesame parser error with rdf:type http://bio2rdf.org/uniprot:Protein
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/bio2rdfpipes.jsp
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From: <p_a...@us...> - 2009-03-18 22:24:04
|
Revision: 221
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=221&view=rev
Author: p_ansell
Date: 2009-03-18 22:23:52 +0000 (Wed, 18 Mar 2009)
Log Message:
-----------
pipes related changes
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/bio2rdfpipes.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/bio2rdf_basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf_subject_object_slicing.pipe
trunk/src/war/WEB-INF/src/operatormapping.xml
Removed Paths:
-------------
trunk/src/war/WEB-INF/src/bio2rdf-basic.pipe
trunk/src/war/WEB-INF/src/bio2rdf-subject-object-slicing.pipe
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From: <p_a...@us...> - 2009-03-18 04:27:21
|
Revision: 220
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=220&view=rev
Author: p_ansell
Date: 2009-03-18 04:27:04 +0000 (Wed, 18 Mar 2009)
Log Message:
-----------
add new pipe example
Added Paths:
-----------
trunk/src/war/WEB-INF/src/bio2rdf-subject-object-slicing.pipe
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From: <p_a...@us...> - 2009-03-18 04:04:07
|
Revision: 219
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=219&view=rev
Author: p_ansell
Date: 2009-03-18 04:03:51 +0000 (Wed, 18 Mar 2009)
Log Message:
-----------
rename and fix pipe definition
Added Paths:
-----------
trunk/src/war/WEB-INF/src/bio2rdf-basic.pipe
Removed Paths:
-------------
trunk/src/war/WEB-INF/src/constructbio2rdf.pipe
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From: <p_a...@us...> - 2009-03-18 01:19:24
|
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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