bio2rdf-svncommits Mailing List for bio2rdf (Page 15)
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From: <p_a...@us...> - 2009-07-29 22:37:36
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Revision: 642
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=642&view=rev
Author: p_ansell
Date: 2009-07-29 22:37:23 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
minor updates to providers and add comment to renderer class
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
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From: <p_a...@us...> - 2009-07-27 07:37:14
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Revision: 641
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=641&view=rev
Author: p_ansell
Date: 2009-07-27 07:37:08 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
remove icons, textual version down the bottom, and computer readable link version up the top
Modified Paths:
--------------
trunk/src/war/WEB-INF/templates/header.vm
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From: <p_a...@us...> - 2009-07-27 07:34:03
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Revision: 640
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=640&view=rev
Author: p_ansell
Date: 2009-07-27 07:33:56 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
make search javascript code work
Modified Paths:
--------------
trunk/src/war/WEB-INF/templates/header.vm
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From: <p_a...@us...> - 2009-07-27 07:22:42
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Revision: 639
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=639&view=rev
Author: p_ansell
Date: 2009-07-27 07:22:31 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
add in more providers, implement manual configuration refresh, add in search box
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/src/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/WEB-INF/templates/header.vm
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/atlas2rdf.jsp
trunk/src/war/debug-configuration.jsp
trunk/src/war/includes-css/html_page_styles.css
trunk/src/war/index.html
trunk/src/war/internalschema.jsp
trunk/src/war/redirectToId.jsp
Added Paths:
-----------
trunk/src/war/manualrefresh.jsp
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From: <p_a...@us...> - 2009-07-27 04:40:46
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Revision: 638
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=638&view=rev
Author: p_ansell
Date: 2009-07-27 04:40:40 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
keep unrecognised statements in a memory buffer so that we don't lose them when the statement is unrecognised
any issues with URI renaming are implementation specific, this just ensures that they don't get lost through lack of a method for keeping them
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
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/RuleTest.java
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From: <p_a...@us...> - 2009-07-27 03:23:20
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Revision: 637
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=637&view=rev
Author: p_ansell
Date: 2009-07-27 03:23:12 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
fix regression with configuration URL interpretation caused by standardising the chosenContentType parameter, where for configuration it was previously named format
Modified Paths:
--------------
trunk/src/war/WEB-INF/urlrewrite.xml
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From: <p_a...@us...> - 2009-07-27 01:14:15
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Revision: 636
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=636&view=rev
Author: p_ansell
Date: 2009-07-27 01:14:07 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
make ntriplesEncoded_endpointSpecificUri work
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/SparqlQueryCreator.java
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From: <p_a...@us...> - 2009-07-27 01:10:13
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Revision: 635
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=635&view=rev
Author: p_ansell
Date: 2009-07-27 01:10:07 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
add duplicate entries for each of the /* entries into robots.txt for the /page/ /rdfxml/ and /n3/ entries so that things aren't bypassed by adding these to the front of URL's
Modified Paths:
--------------
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
trunk/src/war/robots.txt
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From: <p_a...@us...> - 2009-07-26 23:25:14
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Revision: 634
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=634&view=rev
Author: p_ansell
Date: 2009-07-26 23:25:05 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
bump version to beta1 for a few days before releasing
Modified Paths:
--------------
trunk/build.xml
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From: <p_a...@us...> - 2009-07-26 22:20:45
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Revision: 633
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=633&view=rev
Author: p_ansell
Date: 2009-07-26 22:20:39 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
split up preferred response and assumed request content type so that we can still keep assuming application/rdf+xml or text/rdf+n3 in the background without prejudicing the choice of response display format
take out application/xml from the list of types attached to text/html and application/xhtml+xml as it makes common browser accept strings always request rdf+xml even if they have text/html and application/xhtml+xml in the list at higher priorities
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/Bio2RdfContentNegotiator.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/StatisticsEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/atlas2rdf.jsp
trunk/src/war/debug-configuration.jsp
trunk/src/war/error-sesame-output.jsp
trunk/src/war/internalschema.jsp
trunk/src/war/multifetch.jsp
trunk/src/war/serverstats.jsp
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From: <p_a...@us...> - 2009-07-26 08:11:12
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Revision: 632
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=632&view=rev
Author: p_ansell
Date: 2009-07-26 08:11:05 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
fix up definition for ec.bio2rdf.org/sparql to match the recent changes in URI's to the normalised versions
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2009-07-26 07:44:56
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Revision: 631
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=631&view=rev
Author: p_ansell
Date: 2009-07-26 07:44:47 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
make debug-configuration.jsp work with the html renderer and urlrewrite.xml
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/debug-configuration.jsp
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From: <p_a...@us...> - 2009-07-26 06:51:44
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Revision: 630
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=630&view=rev
Author: p_ansell
Date: 2009-07-26 06:51:35 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
fix pfam provider definitions as they have been migrated back to the normalised URI scheme
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
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From: <p_a...@us...> - 2009-07-26 06:28:51
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Revision: 629
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=629&view=rev
Author: p_ansell
Date: 2009-07-26 06:28:41 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
minor changes so that the common accept headers and the final conn neg results will show up in the results... have to decide whether to eliminate application/xml, as it is used by browsers who really want text/html, except they don't realise they don't want xml more than they want text/html
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/log4j.properties
trunk/src/war/atlas2rdf.jsp
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2009-07-26 05:54:07
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Revision: 628
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=628&view=rev
Author: p_ansell
Date: 2009-07-26 05:53:58 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
fix project subproperty mistake
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
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From: <p_a...@us...> - 2009-07-26 05:53:30
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Revision: 627
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=627&view=rev
Author: p_ansell
Date: 2009-07-26 05:53:23 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
add urlrewrite lines so that /page/ /rdfxml/ and /n3/ all work for the internal ontology terms, and fix silly subclass/subproperty mistake
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
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/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/urlrewrite.xml
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2009-07-26 05:22:53
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Revision: 626
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=626&view=rev
Author: p_ansell
Date: 2009-07-26 05:22:47 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
add the project information to the schema jsp page
Modified Paths:
--------------
trunk/src/war/internalschema.jsp
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From: <p_a...@us...> - 2009-07-26 05:21:06
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Revision: 625
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=625&view=rev
Author: p_ansell
Date: 2009-07-26 05:20:52 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
add curation information and a new Project class that will be used to include information about the projects that create resolvers using this package
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/CustomQuery.java
trunk/src/war/WEB-INF/src/org/bio2rdf/NamespaceEntry.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Profile.java
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/RuleTest.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/error-sesame-output.jsp
Added Paths:
-----------
trunk/src/war/WEB-INF/src/org/bio2rdf/Project.java
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From: <p_a...@us...> - 2009-07-26 03:34:38
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Revision: 624
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=624&view=rev
Author: p_ansell
Date: 2009-07-26 03:34:26 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
add some new code that might be useful for improving the performance of matchAndReplaceInputVariablesForQueryType and doReplacementsOnString in SparqlQueryCreator
Modified Paths:
--------------
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/SparqlQueryCreator.java
trunk/src/war/error-sesame-output.jsp
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From: <p_a...@us...> - 2009-07-26 02:16:27
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Revision: 623
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=623&view=rev
Author: p_ansell
Date: 2009-07-26 02:16:21 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
add regex search option, and change all current references to http://bio2rdf.org/query:search so that there is no ambiguity between the virtuoso bif:contains and the sparql regex search method
Modified Paths:
--------------
trunk/src/war/WEB-INF/base-bio2rdf-profiles-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-providers-config.n3
trunk/src/war/WEB-INF/base-bio2rdf-queries-config.n3
trunk/src/war/WEB-INF/my-local-configuration-example.n3
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From: <p_a...@us...> - 2009-07-26 01:48:58
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Revision: 622
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=622&view=rev
Author: p_ansell
Date: 2009-07-26 01:48:52 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
minor changes to add html element to the start of the document
Modified Paths:
--------------
trunk/src/war/WEB-INF/templates/footer.vm
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/atlas2rdf.jsp
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From: <p_a...@us...> - 2009-07-26 01:20:16
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Revision: 621
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=621&view=rev
Author: p_ansell
Date: 2009-07-26 01:20:09 +0000 (Sun, 26 Jul 2009)
Log Message:
-----------
get things working even better, with anchors for all URI's and URL's
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/templates/footer.vm
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/WEB-INF/templates/proptable.vm
Added Paths:
-----------
trunk/src/war/includes-css/html_page_styles.css
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From: <p_a...@us...> - 2009-07-25 23:39:45
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Revision: 620
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=620&view=rev
Author: p_ansell
Date: 2009-07-25 23:39:36 +0000 (Sat, 25 Jul 2009)
Log Message:
-----------
make HTML view display with styles and sort statements, and not show repeating subject triples
Modified Paths:
--------------
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/WEB-INF/templates/proptable.vm
Added Paths:
-----------
trunk/src/war/includes-images/rdf-icon.gif
trunk/src/war/includes-scripts/
trunk/src/war/includes-scripts/script.js
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From: <p_a...@us...> - 2009-07-23 05:19:27
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Revision: 619
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=619&view=rev
Author: p_ansell
Date: 2009-07-23 05:19:23 +0000 (Thu, 23 Jul 2009)
Log Message:
-----------
fix up pubmed rules, and get titles working for the header of the html /page/ version
Modified Paths:
--------------
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/base-bio2rdf-ruletests-config.n3
trunk/src/war/WEB-INF/src/org/bio2rdf/HtmlPageRenderer.java
trunk/src/war/WEB-INF/src/org/bio2rdf/Settings.java
trunk/src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties
trunk/src/war/WEB-INF/templates/header.vm
trunk/src/war/demo.rdf
trunk/src/war/index.html
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From: <p_a...@us...> - 2009-07-23 04:20:12
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Revision: 618
http://bio2rdf.svn.sourceforge.net/bio2rdf/?rev=618&view=rev
Author: p_ansell
Date: 2009-07-23 04:20:09 +0000 (Thu, 23 Jul 2009)
Log Message:
-----------
adjust timeout settings to much lower values
Modified Paths:
--------------
trunk/build.xml
trunk/src/war/WEB-INF/src/org/bio2rdf/RuleTest.java
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