[Gmod-apollo-cmts] CVS: apollo/conf chado-adapter.xml, 1.40, 1.41 rice.tiers, 1.13, 1.14

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/conf
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv15616

Modified Files:
	chado-adapter.xml rice.tiers 
Log Message:
i think scotts commit was all wrong - this is a correction - bad bad scott - naughty!!!



Index: chado-adapter.xml
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/chado-adapter.xml,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** chado-adapter.xml	24 Aug 2007 15:04:56 -0000	1.40
--- chado-adapter.xml	24 Aug 2007 17:32:58 -0000	1.41
***************
*** 3,19 ****
  <chado-adapter>
  
!     <chadoInstance id="flybaseInstance">
  
!         <genePredictionPrograms>
!             <program>genscan</program>
!             <program>piecegenie</program>
!         </genePredictionPrograms>
  
!         <searchHitPrograms>
!            <program>sim4</program>
!            <program>%blastx%</program>
!         </searchHitPrograms>        
  
!         <searchHitsHaveFeatLocs>false</searchHitsHaveFeatLocs>
  
          <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
--- 3,20 ----
  <chado-adapter>
  
!     <chadoInstance id="referenceInstance" default="true">
  
!         <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemplateFile>
  
!         <featureCV>sequence</featureCV>
!         <polypeptideType>polypeptide</polypeptideType>
!         <relationshipCV>relationship</relationshipCV>
!         <propertyTypeCV>feature_property</propertyTypeCV>
  
!         <!-- default is part_of -->
!         <partOfCvTerm>part_of</partOfCvTerm>
!         <transProtRelationTerm>derives_from</transProtRelationTerm>
! 
!         <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
  
          <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
***************
*** 41,47 ****
      </chadoInstance>
  
      <chadoInstance id="riceInstance" default="true">
  
!         <genePredictionPrograms>
              <program>FgenesH</program>
          </genePredictionPrograms>
--- 42,71 ----
      </chadoInstance>
  
+   
      <chadoInstance id="riceInstance" default="true">
  
!        <inheritsInstance>referenceInstance</inheritsInstance>
! 
!         <partOfCvTerm>part_of</partOfCvTerm>
!          <inheritsInstance>referenceInstance</inheritsInstance>
!          <featureCV>sequence</featureCV>
!         <relationshipCV>relationship</relationshipCV>
!         <propertyTypeCV>feature_property</propertyTypeCV>
!         <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile>
! 
!  	<sequenceTypes>
! 	    <type>gene</type>
! 	    <!-- bacs are not in rice yet  <type>BAC</type> -->
! 	    <!-- useStartAndEnd specifies this is a range so that different GUI
! 	         can be used, queryForValue -> query db for chroms/seqIds -->
!             <type>
!                 <name>chromosome</name>
!                 <useStartAndEnd>true</useStartAndEnd>
!                 <queryForValueList>true</queryForValueList>
!                 <isTopLevel>true</isTopLevel>
!             </type>
! 	</sequenceTypes>
! 
!        <genePredictionPrograms>
              <program>FgenesH</program>
          </genePredictionPrograms>
***************
*** 108,111 ****
--- 132,149 ----
      </chadoInstance>    
  
+     <chadoInstance id="ricePure">
+ 
+        <inheritsInstance>riceInstance</inheritsInstance>
+ 
+        <pureJDBCWriteMode>true</pureJDBCWriteMode>
+        <pureJDBCCopyOnWrite>false</pureJDBCCopyOnWrite>
+        <pureJDBCNoCommit>false</pureJDBCNoCommit>
+        <!-- logDirectory>/Users/mgibson/.apollo</logDirectory -->
+        <queryFeatureIdWithUniquename>true</queryFeatureIdWithUniquename>
+        <queryFeatureIdWithName>true</queryFeatureIdWithName>
+    </chadoInstance>    
+    
+ 
+ 
      <!-- Marks Test rice database at brebiou.cshl.org -->
      <chadodb>
***************
*** 150,153 ****
--- 188,215 ----
          <default-command-line-db>true</default-command-line-db>
      </chadodb>
+     <chadodb>
+         <name>dicty hack</name>
+ 	<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
+ 	<url>jdbc:postgresql://gmod.genetics.northwestern.edu:5432/ubuntu</url>
+ 	<dbName>ubuntu</dbName>
+ 	<dbUser>mark</dbUser>
+ 	<dbInstance>riceInstance</dbInstance>
+ 	<style>rice.style</style>
+         <!-- default database to use for loading and saving from -->
+         <!--  command line if none is specified -->
+         <default-command-line-db>true</default-command-line-db>
+     </chadodb>   
+     <chadodb>
+         <name>dicty pure</name>
+ 	<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
+ 	<url>jdbc:postgresql://gmod.genetics.northwestern.edu:5432/ubuntu</url>
+ 	<dbName>ubuntu</dbName>
+ 	<dbUser>mark</dbUser>
+ 	<dbInstance>ricePure</dbInstance>
+ 	<style>rice.style</style>
+         <!-- default database to use for loading and saving from -->
+         <!--  command line if none is specified -->
+         <default-command-line-db>true</default-command-line-db>
+     </chadodb>   
  
  

Index: rice.tiers
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/rice.tiers,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** rice.tiers	5 Apr 2006 05:23:23 -0000	1.13
--- rice.tiers	24 Aug 2007 17:32:58 -0000	1.14
***************
*** 1,4 ****
- # This is the public fly.tiers file for displaying Drosophila
- # melanogaster annotations.
  #
  # This file describes to Apollo how different feature types should be
--- 1,2 ----