[Obo-svn-commit] SF.net SVN: obo: [80] phenote/trunk/conf

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

Revision: 80
Author:   mgibson
Date:     2006-07-28 13:47:19 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=80&view=rev

Log Message:
-----------
added in new pato ontology

Modified Paths:
--------------
    phenote/trunk/conf/initial-flybase.cfg
    phenote/trunk/conf/initial-zfin.cfg
    phenote/trunk/conf/obd.cfg
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/datamodel/Ontology.java
    phenote/trunk/src/java/phenote/gui/AutoComboBox.java
    phenote/trunk/src/web/html/ncbo.html
Modified: phenote/trunk/conf/initial-flybase.cfg
===================================================================
--- phenote/trunk/conf/initial-flybase.cfg	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/conf/initial-flybase.cfg	2006-07-28 20:47:19 UTC (rev 80)
@@ -7,7 +7,7 @@
 
   <entity name="Anatomy" file="fly_anatomy.obo"/>
 
-  <pato file="attribute_and_value.obo"/>
+  <pato file="quality.obo"/>
 
                       
 

Modified: phenote/trunk/conf/initial-zfin.cfg
===================================================================
--- phenote/trunk/conf/initial-zfin.cfg	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/conf/initial-zfin.cfg	2006-07-28 20:47:19 UTC (rev 80)
@@ -6,7 +6,7 @@
 
   <entity name="Anatomy" file="zebrafish_anatomy.obo"/>
 
-  <pato file="attribute_and_value.obo"/>
+  <pato file="quality.obo"/>
 
                       
 

Modified: phenote/trunk/conf/obd.cfg
===================================================================
--- phenote/trunk/conf/obd.cfg	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/conf/obd.cfg	2006-07-28 20:47:19 UTC (rev 80)
@@ -10,7 +10,7 @@
      <ontology name="GO" file="gene_ontology.obo"/>
   </entity>
 
-  <pato file="attribute_and_value.obo"/>
+  <pato file="quality.obo"/>
 
                       
 

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 20:47:19 UTC (rev 80)
@@ -91,6 +91,7 @@
   /** paot config should always be present, make default if not set from xml */
   private FieldConfig getPatoConfig() {
     if (patoConfig == null) {
+      System.out.println("error pato config is null, making default");
       OntologyConfig o = OntologyConfig.defaultPato;
       patoConfig = new FieldConfig(CharFieldEnum.PATO,o);
     }
@@ -252,7 +253,8 @@
   private void parsePato(Node node) {
     if (!node.getNodeName().equals("pato")) return;
     OntologyConfig oc = makeOntologyConfig(node,"Pato");
-    getPatoConfig().addOntologyConfig(oc);
+    //getPatoConfig().addOntologyConfig(oc);
+    patoConfig = new FieldConfig(CharFieldEnum.PATO,oc);
   }
 
   private void parseEntity(Node node) {

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2006-07-28 20:47:19 UTC (rev 80)
@@ -101,8 +101,9 @@
 
       // SKIP PATO ATTRIBUTES - only want values - or do !contains "value"?
       // yes do contains value - as theres other crap to filter too
-      if (filterAttributes() && isAttribute(originalTerm))
-        continue;
+      // apparently curators want to see attribs as well according to Michael
+      //if (filterAttributes() && isAttribute(originalTerm))
+      //continue;
 
       if (searchParams.searchTerms()) {
         // adds originalTerm to searchTerms if match (1st if exact)
@@ -142,7 +143,7 @@
   }
            
   // part of search params?
-  private boolean filterAttributes() { return isPato(); }
+  //private boolean filterAttributes() { return isPato(); }
 
   // make enum!!
   private boolean isPato() {

Modified: phenote/trunk/src/java/phenote/gui/AutoComboBox.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/AutoComboBox.java	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/src/java/phenote/gui/AutoComboBox.java	2006-07-28 20:47:19 UTC (rev 80)
@@ -133,6 +133,8 @@
   /** This gets obo class selected in completion list - not from text box 
       Returns null if nothing selected - can happen amidst changing selection */
   private OBOClass getSelectedCompListOboClass() {
+    if (defaultComboBoxModel == null)
+      return null;
     Object obj = defaultComboBoxModel.getSelectedItem();
     if (obj == null)
       return null;

Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-28 20:16:25 UTC (rev 79)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-28 20:47:19 UTC (rev 80)
@@ -67,7 +67,7 @@
 
          <fieldset class="search">
             <br/><br/><br/>
-            <label>PATO: </label>
+            <label>Quality: </label>
 
             <!-- input autocomplete="off" id="ontologyname" name="ontologyname" size="20" type="text" value="" / -->
             <input autocomplete="off" id="patoInput" name="patoInput" size="20" type="text" value="" />


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