[MOBY-guts] biomoby commit

Paul Gordon gordonp at dev.open-bio.org
Wed Mar 17 20:21:55 UTC 2010 

gordonp
Wed Mar 17 16:21:55 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv11511/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	moby2HTML.xsl mobyBuilderRules.xml 
Log Message:
Interface updates related to new search/filter and workflow generation/preview functions
moby-live/Java/src/main/ca/ucalgary/seahawk/resources moby2HTML.xsl,1.4,1.5 mobyBuilderRules.xml,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/moby2HTML.xsl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/moby2HTML.xsl	2007/07/28 03:47:41	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/moby2HTML.xsl	2010/03/17 20:21:55	1.5
@@ -218,18 +218,20 @@
 
   <!-- Base Object class, has a namespace and ID. That's it. -->
   <xsl:template match="moby:Object | mobys:Object | Object" mode="elucidate">
-    <a href="http://moby/{@moby:namespace | @mobys:namespace | @namespace}?id={@moby:id | @mobys:id | @id}&amp;name={@moby:articleName | @mobys:articleName | @articleName}">ID <xsl:value-of select="@moby:namespace | @mobys:namespace | @namespace"/>:<xsl:value-of select="@moby:id | @mobys:id | @id"/> (<xsl:value-of select="@moby:articleName | @mobys:articleName | @articleName"/>)</a><xsl:text> </xsl:text>
+    <xsl:variable name="xptr"><xsl:call-template name="getXPointer"/></xsl:variable>
+    <a href="{$sourceURL}#{$xptr}">ID <xsl:value-of select="@moby:namespace | @mobys:namespace | @namespace"/>:<xsl:value-of select="@moby:id | @mobys:id | @id"/> (<xsl:value-of select="@moby:articleName | @mobys:articleName | @articleName"/>)</a><xsl:text> </xsl:text>
     <xsl:apply-templates select="moby:CrossReference | mobys:CrossReference | CrossReference" mode="elucidate"/>
-  </xsl:template> <!-- end Object template -->
+  </xsl:template>  <!-- end Object template -->
 
   <xsl:template match="moby:String | mobys:String | String" mode="elucidate">
     <xsl:variable name="xptr"><xsl:call-template name="getXPointer"/></xsl:variable>
     <a href="{$sourceURL}#{$xptr}">String <xsl:if test="string-length(@moby:namespace | @mobys:namespace | @namespace)"><xsl:value-of select="@moby:namespace | @mobys:namespace | @namespace"/>:</xsl:if><xsl:if test="string-length(@moby:id | @mobys:id | @id)"><xsl:value-of select="@moby:id | @mobys:id | @id"/> </xsl:if>(<xsl:value-of select="@moby:articleName | @mobys:articleName | @articleName"/>)</a>: <xsl:value-of select="."/><br/>
     <xsl:apply-templates select="moby:CrossReference | mobys:CrossReference | CrossReference" mode="elucidate"/>
-  </xsl:template> <!-- end String template -->
+  </xsl:template>  <!-- end String template -->
 
   <xsl:template match="moby:Integer | mobys:Integer | Integer | moby:Float | mobys:Float | Float | moby:Boolean | mobys:Boolean | Boolean | moby:DateTime | mobys:DateTime | DateTime" mode="elucidate">
-    <xsl:value-of select="@moby:articleName | @mobys:articleName | @articleName"/>: <xsl:value-of select="."/><br/>
+    <xsl:variable name="xptr"><xsl:call-template name="getXPointer"/></xsl:variable>
+    <a href="{$sourceURL}#{$xptr}"><xsl:value-of select="@moby:articleName | @mobys:articleName | @articleName"/></a> (<xsl:value-of select="local-name(.)"/>): <xsl:value-of select="."/><br/>
   </xsl:template> <!-- end Integer template -->
 
   <!-- Should match more complex objects -->

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2009/08/17 21:31:52	1.9
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2010/03/17 20:21:55	1.10
@@ -3,6 +3,9 @@
 <prefix value="agave">http://www.bioxml.info/dtd/agave.dtd</prefix>
 <prefix value="tigr">http://www.bioxml.info/dtd/tigrxml.dtd</prefix>
 <prefix value="bioseq">http://www.bioxml.info/dtd/Bioseq.dtd</prefix>
+<prefix value="bmcarticle">http://www.biomedcentral.com/xml/article.dtd</prefix>
+<prefix value="ncbiarticle">http://dtd.nlm.nih.gov/publishing/2.0/journalpublishing.dtd</prefix>
+<prefix value="gpml">http://genmapp.org/GPML/2008a</prefix>
 
 <object>
 <regex>(HEADER\s+.*?(\S+)\n
@@ -98,10 +101,11 @@
 
 <!-- A Link object, representing a URL -->
 <object>
+  <dc:source>urn:lsid:bioxml.info:mobyLiftingSchemaMapping:URL2Link</dc:source>
   <regex>((?:http|ftp|file)://
          ([^/\x20\r\t\n]+)?     # host name (non-whitespace, non-slash), maybe
          \S*?)                  # rest of the URL until
-         ([,\.\)\(]\s|\z)       # trailing punctuation and whitespace, or just EOD
+         ([,\.\)\(]?\s|\z)      # trailing punctuation and whitespace, or just EOD
          </regex>
   <namespace>
     <ns value="URL">$1</ns>
@@ -140,6 +144,28 @@
   </namespace>
 </object>
 
+<object>
+  <xpath>bmcarticle:pubid[@idtype="pmpid"]/text()</xpath>
+  <namespace>
+    <ns value="PMID">$1</ns>
+  </namespace>
+</object>
+
+<object>
+  <xpath>bmcarticle:pubid[@idtype="doi"]/text()</xpath>
+  <namespace>
+    <ns value="DOI" model="http://bio2rdf.org/ns:doi">$1</ns>
+  </namespace>
+</object>
+
+<object>
+  <xpath>ncbiarticle:article-id[@pub-id-type="doi"]/text()</xpath>
+  <namespace>
+    <ns value="DOI" model="http://bio2rdf.org/ns:doi">$1</ns>
+  </namespace>
+</object>
+
+
 <!-- NCBI COGs -->
 <object>
   <regex>(?:[KC]OG|[kc]og):?\s*(\d{4})</regex>
@@ -153,7 +179,7 @@
   <dc:source>urn:lsid:bioxml.info:mobyLiftingSchemaMapping:prefixedDOI2DOI</dc:source>
   <regex>(?:DOI|doi|[Dd]igital\s+[Oo]bject\s+[Ii][Dd](?:entifier))\s*:?\s*(10\.\d+/[^%"\#\x20\t\r\n]+)</regex>
   <namespace>
-    <ns value="DOI">$1</ns>
+    <ns value="DOI" model="http://bio2rdf.org/ns:doi">$1</ns>
   </namespace>
 </object>
 
@@ -218,6 +244,14 @@
   </namespace>
 </object>
 
+<!-- gets a wikipathways entry's cross-references to NCBI Entrez gene -->
+<object>
+  <xpath>gpml:Xref[@Database="Entrez Gene"]/@ID</xpath>
+  <namespace>
+    <ns value="EntrezGene_EntrezGeneID">$1</ns>
+  </namespace>
+</object>
+
 <!-- NCBI Reference Sequence -->
 <object>
   <regex>([NXYZ][CMP]_\d{6})</regex>

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